From e57ecd87bf2b0d3c9bac5e06ecb10cde903864d5 Mon Sep 17 00:00:00 2001 From: mvdoc <> Date: Wed, 13 Apr 2022 01:34:28 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20gallantl?= =?UTF-8?q?ab/pycortex@c75852de3f66aa947054f08d7da16e6a39ebbdcb=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .buildinfo | 2 +- .../plot_make_gif.ipynb | 2 +- .../static_with_custom_template.ipynb | 2 +- .../auto_examples_python.zip | Bin 73840 -> 73836 bytes .../plot_roi_voxel_index_volume.ipynb | 2 +- .../multiple_datasets.ipynb | 2 +- .../plot_get_roi_vertices.ipynb | 2 +- .../plot_thickness_nanmean.ipynb | 2 +- .../static.ipynb | 2 +- .../plot_voxel_distance_from_surface.ipynb | 2 +- .../plot_subsurfaces.ipynb | 2 +- .../plot_dropout.ipynb | 2 +- .../plot_roi_voxel_mask.ipynb | 2 +- .../plot_connected_vertices.ipynb | 2 +- .../retinotopy_webgl.ipynb | 2 +- .../multi_panels_plots.ipynb | 2 +- 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4 +- generated/cortex.volume.unmask.html | 4 +- generated/cortex.webgl.make_static.html | 4 +- generated/cortex.webgl.show.html | 4 +- generated/cortex.xfm.Transform.html | 8 +- genindex.html | 4 +- index.html | 4 +- install.html | 4 +- py-modindex.html | 4 +- rois.html | 4 +- search.html | 4 +- searchindex.js | 2 +- segmentation.html | 4 +- segmentation_guide.html | 4 +- transforms.html | 4 +- userguide/webgl.html | 4 +- 406 files changed, 1434 insertions(+), 1363 deletions(-) diff --git a/.buildinfo b/.buildinfo index 1711d72ec..dfc8a79db 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 9cad32f555da1c40107965e6987fd25e +config: 13b17c5c373045c1725623acad9b96b1 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_downloads/0171ca85d45eca4cef1870c2e499de10/plot_make_gif.ipynb b/_downloads/0171ca85d45eca4cef1870c2e499de10/plot_make_gif.ipynb index fa7bc1ff4..99d239e2e 100644 --- a/_downloads/0171ca85d45eca4cef1870c2e499de10/plot_make_gif.ipynb +++ b/_downloads/0171ca85d45eca4cef1870c2e499de10/plot_make_gif.ipynb @@ -125,7 +125,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/03727e1a4b42addea2598e45140498aa/static_with_custom_template.ipynb b/_downloads/03727e1a4b42addea2598e45140498aa/static_with_custom_template.ipynb index 5dd028c78..88cc5ca81 100644 --- a/_downloads/03727e1a4b42addea2598e45140498aa/static_with_custom_template.ipynb +++ b/_downloads/03727e1a4b42addea2598e45140498aa/static_with_custom_template.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index 9d58005986eb23336f8325fe5f6546629b063a17..4a86a80ba97d8bce16a3ba76ab3735023906ca6b 100644 GIT binary patch delta 1840 zcmY*Z4NTN!7=Pb;|91!6oie;TK8`#7n8E-}L`y4OQ*umkLiNuUec?wj1q&5*WP+Mz zRD|tcK86Z9V``fQW2TlGN>0O!14reQ{KSbQ;a0QdWc}X1eZ9B+Zohlp=Xvh=9%#{i zY0*6SxkB?Y`FYA!-TYN>mL`fo7EhcXDdvN?hkxM|&x33p_k$+pxT>2xK8JV}g17xy zPEibUA}t&#Nb5$Epztwd(#m<;SG9#CtKhPXCb(d(~Kdp+3cBrP#XtIlw zAXyawr|1D$zU)whSPN1&`)eW2fSk{3afot|{PkNj0l&>ta<1CM8jzfMJwmJpnN*Ul zi9V3Rf@=|CCCGx(D7#n%GNuTmAEdu3Y!|mc8a_U#S(0Nlm+fMdySllt{`UwG4bpe; z*GQ2Ja(SOKN@yUvcR%b9w_#OSJIii^p!@iCr+5hDx$Xu{Oaxio*5MH2L9X^U+AN9D 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zfG&8HXKNM|b5keGl7wILvz=gYc=9UnJFnoT zkPDKRhoUtQ!ZfjG)A+YtFvBFg{UNFmqBK!qS-{;FLNq^&+3l5)WFhpcl0sAn^vUXi;QE^6bZe~nw!KU{uBM%G3)8oN=P{rZl0pO)oFnpQm z8$BWJI3j{}Oz!o(tQ%(7hxx*jq7JIonkn#VH>wnKZ^=$wE diff --git a/_downloads/712cc7a3913a50341baae9f6b000d797/plot_mosaic.ipynb b/_downloads/712cc7a3913a50341baae9f6b000d797/plot_mosaic.ipynb index 8c807c1ae..0fccb125d 100644 --- a/_downloads/712cc7a3913a50341baae9f6b000d797/plot_mosaic.ipynb +++ b/_downloads/712cc7a3913a50341baae9f6b000d797/plot_mosaic.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/71eedfa1e15eeae1d50e837a5d00378d/plot_tissots_indicatrix.ipynb b/_downloads/71eedfa1e15eeae1d50e837a5d00378d/plot_tissots_indicatrix.ipynb index 878b95d43..ecff2a48f 100644 --- a/_downloads/71eedfa1e15eeae1d50e837a5d00378d/plot_tissots_indicatrix.ipynb +++ b/_downloads/71eedfa1e15eeae1d50e837a5d00378d/plot_tissots_indicatrix.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/774806b543a93da25908653d426c15c1/plot_cutouts.ipynb b/_downloads/774806b543a93da25908653d426c15c1/plot_cutouts.ipynb index 53ff32db2..0a760c45c 100644 --- a/_downloads/774806b543a93da25908653d426c15c1/plot_cutouts.ipynb +++ b/_downloads/774806b543a93da25908653d426c15c1/plot_cutouts.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/813e10fd805fb08e209798753ce45729/plot_volume_to_vertex.ipynb b/_downloads/813e10fd805fb08e209798753ce45729/plot_volume_to_vertex.ipynb index 26f167731..7b862fdeb 100644 --- a/_downloads/813e10fd805fb08e209798753ce45729/plot_volume_to_vertex.ipynb +++ b/_downloads/813e10fd805fb08e209798753ce45729/plot_volume_to_vertex.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/85a1ab66519fd897a9f08ef615f4ac6b/plot_sulci.ipynb b/_downloads/85a1ab66519fd897a9f08ef615f4ac6b/plot_sulci.ipynb index 235f3a42f..c427e69f8 100644 --- a/_downloads/85a1ab66519fd897a9f08ef615f4ac6b/plot_sulci.ipynb +++ b/_downloads/85a1ab66519fd897a9f08ef615f4ac6b/plot_sulci.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/88045a5ca44795160381b3e40115ed85/plot_vertexRGB.ipynb b/_downloads/88045a5ca44795160381b3e40115ed85/plot_vertexRGB.ipynb index abe253678..15959159f 100644 --- a/_downloads/88045a5ca44795160381b3e40115ed85/plot_vertexRGB.ipynb +++ b/_downloads/88045a5ca44795160381b3e40115ed85/plot_vertexRGB.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/8cf11f78d8c4186f5276b30e9ad94586/plot_vertex2D.ipynb b/_downloads/8cf11f78d8c4186f5276b30e9ad94586/plot_vertex2D.ipynb index f9c501ca9..9676ad756 100644 --- a/_downloads/8cf11f78d8c4186f5276b30e9ad94586/plot_vertex2D.ipynb +++ b/_downloads/8cf11f78d8c4186f5276b30e9ad94586/plot_vertex2D.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/93df78f3116af947a5f503a4a33c9ddd/plot_make_svg.ipynb b/_downloads/93df78f3116af947a5f503a4a33c9ddd/plot_make_svg.ipynb index 217095a9c..c540a6ab5 100644 --- a/_downloads/93df78f3116af947a5f503a4a33c9ddd/plot_make_svg.ipynb +++ b/_downloads/93df78f3116af947a5f503a4a33c9ddd/plot_make_svg.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/967bde64d496491cb07a443c9ede7fc9/plot_advanced_compositing.ipynb b/_downloads/967bde64d496491cb07a443c9ede7fc9/plot_advanced_compositing.ipynb index 5c462d26e..21006a193 100644 --- a/_downloads/967bde64d496491cb07a443c9ede7fc9/plot_advanced_compositing.ipynb +++ b/_downloads/967bde64d496491cb07a443c9ede7fc9/plot_advanced_compositing.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/a075cfaa8cd8b107253dda362b33178e/plot_flatmap_distortion.ipynb b/_downloads/a075cfaa8cd8b107253dda362b33178e/plot_flatmap_distortion.ipynb index fbc14208f..afb5e4cec 100644 --- a/_downloads/a075cfaa8cd8b107253dda362b33178e/plot_flatmap_distortion.ipynb +++ b/_downloads/a075cfaa8cd8b107253dda362b33178e/plot_flatmap_distortion.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/bcb26d7471e165be66ecc1ea4a79a747/import_fmriprep.ipynb b/_downloads/bcb26d7471e165be66ecc1ea4a79a747/import_fmriprep.ipynb index 5b0f71ad9..43cdc1819 100644 --- a/_downloads/bcb26d7471e165be66ecc1ea4a79a747/import_fmriprep.ipynb +++ b/_downloads/bcb26d7471e165be66ecc1ea4a79a747/import_fmriprep.ipynb @@ -26,7 +26,7 @@ }, "outputs": [], "source": [ - "import cortex\nfrom cortex import fmriprep\nfrom os import path as op\n\n# Location of the downloaded openfmri dataset\nsource_directory = '/derivatives/ds000164'\n# fmriprep subject name (without \"sub-\")\nsubject_id = '001' \n\n# import subject into pycortex database\nfmriprep.import_subj(subject_id, source_directory)\n\n# We can use visualize the imported subject's T1-weighted image\nanat_nifti = 'fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz'\nt1_image_path = op.join(source_directory, anat_nifti)\n\n# Now we can make a volume using the built-in identity transform\nt1w_volume = cortex.Volume(t1_image_path, subject_id, 'identity')\n\n# And show the result.\nds = cortex.Dataset(t1w=t1w_volume)\ncortex.webgl.show(ds)" + "import cortex\nfrom cortex import fmriprep\nfrom os import path as op\n\n# Location of the downloaded openfmri dataset\nsource_directory = '/derivatives/ds000164'\n# fmriprep subject name (without \"sub-\")\nsubject_id = '001' \n\n# import subject into pycortex database\nfmriprep.import_subj(subject_id, source_directory)\n\n# We can visualize the imported subject's T1-weighted image\nanat_nifti = 'fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz'\nt1_image_path = op.join(source_directory, anat_nifti)\n\n# Now we can make a volume using the built-in identity transform\nt1w_volume = cortex.Volume(t1_image_path, subject_id, 'identity')\n\n# And show the result.\nds = cortex.Dataset(t1w=t1w_volume)\ncortex.webgl.show(ds)" ] } ], @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/c47834bb21df7cc049ba6afc8a9f9184/plot_dataset_arithmetic.ipynb b/_downloads/c47834bb21df7cc049ba6afc8a9f9184/plot_dataset_arithmetic.ipynb index 723f3abe3..8164e92e2 100644 --- a/_downloads/c47834bb21df7cc049ba6afc8a9f9184/plot_dataset_arithmetic.ipynb +++ b/_downloads/c47834bb21df7cc049ba6afc8a9f9184/plot_dataset_arithmetic.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/c4a1569322d832cb845e73fb64382cd3/plot_volume2D.ipynb b/_downloads/c4a1569322d832cb845e73fb64382cd3/plot_volume2D.ipynb index 2581e2984..e8c76002a 100644 --- a/_downloads/c4a1569322d832cb845e73fb64382cd3/plot_volume2D.ipynb +++ b/_downloads/c4a1569322d832cb845e73fb64382cd3/plot_volume2D.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/c74b122a2f122b3931ba518c8dce3b97/mni_to_subject.ipynb b/_downloads/c74b122a2f122b3931ba518c8dce3b97/mni_to_subject.ipynb index b46140dd9..4a8443b5e 100644 --- a/_downloads/c74b122a2f122b3931ba518c8dce3b97/mni_to_subject.ipynb +++ b/_downloads/c74b122a2f122b3931ba518c8dce3b97/mni_to_subject.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/cc502342f659cf0c536754003ffae538/dynamic_with_custom_template.ipynb b/_downloads/cc502342f659cf0c536754003ffae538/dynamic_with_custom_template.ipynb index 61d561158..b1d29b54e 100644 --- a/_downloads/cc502342f659cf0c536754003ffae538/dynamic_with_custom_template.ipynb +++ b/_downloads/cc502342f659cf0c536754003ffae538/dynamic_with_custom_template.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/d9b4e151ce75aace67a450abc15967b6/plot_make_png.ipynb b/_downloads/d9b4e151ce75aace67a450abc15967b6/plot_make_png.ipynb index 6c56acad2..3b6b75134 100644 --- a/_downloads/d9b4e151ce75aace67a450abc15967b6/plot_make_png.ipynb +++ b/_downloads/d9b4e151ce75aace67a450abc15967b6/plot_make_png.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/dafaff1c5c813c5150e44a7314911857/plot_volumeRGB.ipynb b/_downloads/dafaff1c5c813c5150e44a7314911857/plot_volumeRGB.ipynb index 38c5f9913..86f856fb9 100644 --- a/_downloads/dafaff1c5c813c5150e44a7314911857/plot_volumeRGB.ipynb +++ b/_downloads/dafaff1c5c813c5150e44a7314911857/plot_volumeRGB.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/e01e45ad3d31a19a9f9f8dff3847cf51/plot_zoom_to_roi.ipynb b/_downloads/e01e45ad3d31a19a9f9f8dff3847cf51/plot_zoom_to_roi.ipynb index 06cf91584..e61efbe07 100644 --- a/_downloads/e01e45ad3d31a19a9f9f8dff3847cf51/plot_zoom_to_roi.ipynb +++ b/_downloads/e01e45ad3d31a19a9f9f8dff3847cf51/plot_zoom_to_roi.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/efc62904d6eba92714248fce62fca073/single_dataset.ipynb b/_downloads/efc62904d6eba92714248fce62fca073/single_dataset.ipynb index 791277c39..97df1aafe 100644 --- a/_downloads/efc62904d6eba92714248fce62fca073/single_dataset.ipynb +++ b/_downloads/efc62904d6eba92714248fce62fca073/single_dataset.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/f23fbcea3c616b715df90ee0cbac9bdf/plot_geodesic_path.ipynb b/_downloads/f23fbcea3c616b715df90ee0cbac9bdf/plot_geodesic_path.ipynb index a6d91f2d3..c929d6152 100644 --- a/_downloads/f23fbcea3c616b715df90ee0cbac9bdf/plot_geodesic_path.ipynb +++ b/_downloads/f23fbcea3c616b715df90ee0cbac9bdf/plot_geodesic_path.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_downloads/fc8b05be95bda3f3431b5b5752f2c0fd/plot_geodesic_distance.ipynb b/_downloads/fc8b05be95bda3f3431b5b5752f2c0fd/plot_geodesic_distance.ipynb index afac7eeee..5ff5df1de 100644 --- a/_downloads/fc8b05be95bda3f3431b5b5752f2c0fd/plot_geodesic_distance.ipynb +++ b/_downloads/fc8b05be95bda3f3431b5b5752f2c0fd/plot_geodesic_distance.ipynb @@ -46,7 +46,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.10" + "version": "3.9.12" } }, "nbformat": 4, diff --git a/_modules/cortex/align.html b/_modules/cortex/align.html index 32bbe6c7b..feef1b67d 100644 --- a/_modules/cortex/align.html +++ b/_modules/cortex/align.html @@ -5,7 +5,7 @@ - cortex.align — pycortex 1.2.3 documentation + cortex.align — pycortex 1.2.4 documentation @@ -42,7 +42,7 @@

Source code for cortex.align

 from builtins import input
 import warnings
 
-
[docs]def manual(subject, xfmname, reference=None, **kwargs): +def mayavi_manual(subject, xfmname, reference=None, **kwargs): """Open GUI for manually aligning a functional volume to the cortical surface for `subject`. This creates a new transform called `xfm`. The name of a nibabel-readable file (e.g. nii) should be supplied as `reference`. This image will be copied into the database. @@ -73,6 +73,13 @@

Source code for cortex.align

     m : 2D ndarray, shape (4, 4)
         Transformation matrix.
     """
+
+    warnings.warn("This is the old cortex.align.manual(), and has been "
+                  "deprecated. Please use the new cortex.align.manual() "
+                  "(previously cortex.align.fs_manual()), which uses "
+                  "the `freeview` program in the freesurfer suite, to "
+                  "perform manual alignment.", DeprecationWarning
+                  )
     from .database import db
     from .mayavi_aligner import get_aligner
     def save_callback(aligner):
@@ -118,9 +125,18 @@ 

Source code for cortex.align

     m.save_callback = view_callback if view_only_mode else save_callback
     m.configure_traits()
 
-    return m
+ return m + + +def fs_manual(subject, xfmname, **kwargs): + """Legacy name for cortex.align.manual. Please use that function, and see the help there.""" + warnings.warn(("Deprecated name - function has been renamed cortex.align.manual" + "This function name will be removed in a future release." + ), DeprecationWarning) + return manual(subject, xfmname, **kwargs) -def fs_manual(subject, xfmname, output_name="register.lta", wm_color="yellow", + +
[docs]def manual(subject, xfmname, output_name="register.lta", wm_color="yellow", pial_color="blue", wm_surface='white', noclean=False, reference=None, inspect_only=False): """Open Freesurfer FreeView GUI for manually aligning/adjusting a functional volume to the cortical surface for `subject`. This creates a new transform @@ -139,6 +155,9 @@

Source code for cortex.align

     ALSO: all the freesurfer environment stuff shouldn't be necessary, except that
     I don't know what vox2ras-tkr is doing.
 
+    Renamed from fs_manual() to manual(), since old manual() function was no longer 
+    supported (or functional) for a while due to changes in mayavi.
+
 
     Parameters
     ----------
@@ -250,7 +269,7 @@ 

Source code for cortex.align

             shutil.rmtree(cache)
         else:
             retval = cache
-    return retval
+    return retval
[docs]def automatic(subject, xfmname, reference, noclean=False, bbrtype="signed", @@ -491,7 +510,7 @@

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diff --git a/_modules/cortex/anat.html b/_modules/cortex/anat.html index 32304ab3d..d3e060eb3 100644 --- a/_modules/cortex/anat.html +++ b/_modules/cortex/anat.html @@ -5,7 +5,7 @@ - cortex.anat — pycortex 1.2.3 documentation + cortex.anat — pycortex 1.2.4 documentation @@ -196,7 +196,7 @@

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diff --git a/_modules/cortex/database.html b/_modules/cortex/database.html index 78b44f28d..d49fe06f7 100644 --- a/_modules/cortex/database.html +++ b/_modules/cortex/database.html @@ -5,7 +5,7 @@ - cortex.database — pycortex 1.2.3 documentation + cortex.database — pycortex 1.2.4 documentation @@ -924,7 +924,7 @@

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diff --git a/_modules/cortex/dataset/view2D.html b/_modules/cortex/dataset/view2D.html index 365e80809..27f7cc4b0 100644 --- a/_modules/cortex/dataset/view2D.html +++ b/_modules/cortex/dataset/view2D.html @@ -5,7 +5,7 @@ - cortex.dataset.view2D — pycortex 1.2.3 documentation + cortex.dataset.view2D — pycortex 1.2.4 documentation @@ -379,7 +379,7 @@

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diff --git a/_modules/cortex/dataset/viewRGB.html b/_modules/cortex/dataset/viewRGB.html index fd81526f9..827837f7f 100644 --- a/_modules/cortex/dataset/viewRGB.html +++ b/_modules/cortex/dataset/viewRGB.html @@ -5,7 +5,7 @@ - cortex.dataset.viewRGB — pycortex 1.2.3 documentation + cortex.dataset.viewRGB — pycortex 1.2.4 documentation @@ -655,7 +655,7 @@

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diff --git a/_modules/cortex/dataset/views.html b/_modules/cortex/dataset/views.html index d0da35546..fab6703f5 100644 --- a/_modules/cortex/dataset/views.html +++ b/_modules/cortex/dataset/views.html @@ -5,7 +5,7 @@ - cortex.dataset.views — pycortex 1.2.3 documentation + cortex.dataset.views — pycortex 1.2.4 documentation @@ -501,7 +501,7 @@

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©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 diff --git a/_modules/cortex/freesurfer.html b/_modules/cortex/freesurfer.html index 4908ec08b..05771efe1 100644 --- a/_modules/cortex/freesurfer.html +++ b/_modules/cortex/freesurfer.html @@ -5,7 +5,7 @@ - cortex.freesurfer — pycortex 1.2.3 documentation + cortex.freesurfer — pycortex 1.2.4 documentation @@ -316,7 +316,8 @@

Source code for cortex.freesurfer

     database.db.clear_cache(cx_subject)
     # Remove overlays.svg file (FLATMAPS HAVE CHANGED)
     overlays_file = database.db.get_paths(cx_subject)['overlays']
-    os.unlink(overlays_file)
+ if os.path.exists(overlays_file): + os.unlink(overlays_file) # Regenerate it? @@ -1318,7 +1319,7 @@

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©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 diff --git a/_sources/auto_examples/datasets/plot_dataset_arithmetic.rst.txt b/_sources/auto_examples/datasets/plot_dataset_arithmetic.rst.txt index 94ba5ad24..e0a541614 100644 --- a/_sources/auto_examples/datasets/plot_dataset_arithmetic.rst.txt +++ b/_sources/auto_examples/datasets/plot_dataset_arithmetic.rst.txt @@ -66,17 +66,17 @@ normal arithmetic operators like +, -, *, /, and ** Generating a flatmap cache Failed to get connection - ** (inkscape:4987): CRITICAL **: 21:01:15.132: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:4987): CRITICAL **: 21:01:15.132: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:4987): CRITICAL **: 21:01:15.132: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5116): CRITICAL **: 01:26:49.265: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5116): CRITICAL **: 01:26:49.265: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5116): CRITICAL **: 01:26:49.265: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:4990): CRITICAL **: 21:01:16.307: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:4990): CRITICAL **: 21:01:16.307: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:4990): CRITICAL **: 21:01:16.307: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5119): CRITICAL **: 01:26:50.304: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5119): CRITICAL **: 01:26:50.304: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5119): CRITICAL **: 01:26:50.304: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:4994): CRITICAL **: 21:01:17.382: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:4994): CRITICAL **: 21:01:17.382: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:4994): CRITICAL **: 21:01:17.382: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5122): CRITICAL **: 01:26:51.342: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5122): CRITICAL **: 01:26:51.342: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5122): CRITICAL **: 01:26:51.342: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -119,7 +119,7 @@ normal arithmetic operators like +, -, *, /, and ** .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 20.591 seconds) + **Total running time of the script:** ( 0 minutes 18.572 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_dataset_arithmetic.py: diff --git a/_sources/auto_examples/datasets/plot_vertex.rst.txt b/_sources/auto_examples/datasets/plot_vertex.rst.txt index 3254a3bca..18370e858 100644 --- a/_sources/auto_examples/datasets/plot_vertex.rst.txt +++ b/_sources/auto_examples/datasets/plot_vertex.rst.txt @@ -66,13 +66,13 @@ filled in with zeros. .. code-block:: none Failed to get connection - ** (inkscape:5026): CRITICAL **: 21:01:39.856: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5026): CRITICAL **: 21:01:39.856: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5026): CRITICAL **: 21:01:39.856: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5153): CRITICAL **: 01:27:09.888: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5153): CRITICAL **: 01:27:09.888: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5153): CRITICAL **: 01:27:09.888: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5030): CRITICAL **: 21:01:40.896: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5030): CRITICAL **: 21:01:40.896: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5030): CRITICAL **: 21:01:40.896: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5156): CRITICAL **: 01:27:10.878: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5156): CRITICAL **: 01:27:10.878: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5156): CRITICAL **: 01:27:10.878: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -121,7 +121,7 @@ filled in with zeros. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 5.277 seconds) + **Total running time of the script:** ( 0 minutes 4.388 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_vertex.py: diff --git a/_sources/auto_examples/datasets/plot_vertex2D.rst.txt b/_sources/auto_examples/datasets/plot_vertex2D.rst.txt index 44d0c2dac..2e77d0ebc 100644 --- a/_sources/auto_examples/datasets/plot_vertex2D.rst.txt +++ b/_sources/auto_examples/datasets/plot_vertex2D.rst.txt @@ -50,9 +50,9 @@ the length of the all the vertices in the subject. .. code-block:: none Failed to get connection - ** (inkscape:5035): CRITICAL **: 21:01:45.259: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5035): CRITICAL **: 21:01:45.259: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5035): CRITICAL **: 21:01:45.259: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5161): CRITICAL **: 01:27:14.312: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5161): CRITICAL **: 01:27:14.312: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5161): CRITICAL **: 01:27:14.312: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -98,7 +98,7 @@ the length of the all the vertices in the subject. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 2.318 seconds) + **Total running time of the script:** ( 0 minutes 1.972 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_vertex2D.py: diff --git a/_sources/auto_examples/datasets/plot_vertexRGB.rst.txt b/_sources/auto_examples/datasets/plot_vertexRGB.rst.txt index 231f7a269..e8a98f9d1 100644 --- a/_sources/auto_examples/datasets/plot_vertexRGB.rst.txt +++ b/_sources/auto_examples/datasets/plot_vertexRGB.rst.txt @@ -51,9 +51,9 @@ use any cortex.Vertex objects in their place though. .. code-block:: none Failed to get connection - ** (inkscape:5052): CRITICAL **: 21:01:55.664: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5052): CRITICAL **: 21:01:55.664: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5052): CRITICAL **: 21:01:55.664: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5177): CRITICAL **: 01:27:22.876: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5177): CRITICAL **: 01:27:22.876: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5177): CRITICAL **: 01:27:22.876: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -116,7 +116,7 @@ use any cortex.Vertex objects in their place though. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 2.322 seconds) + **Total running time of the script:** ( 0 minutes 1.988 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_vertexRGB.py: diff --git a/_sources/auto_examples/datasets/plot_volume.rst.txt b/_sources/auto_examples/datasets/plot_volume.rst.txt index d69765771..936b7cac7 100644 --- a/_sources/auto_examples/datasets/plot_volume.rst.txt +++ b/_sources/auto_examples/datasets/plot_volume.rst.txt @@ -72,17 +72,17 @@ on the brain. .. code-block:: none Failed to get connection - ** (inkscape:5012): CRITICAL **: 21:01:31.654: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5012): CRITICAL **: 21:01:31.654: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5012): CRITICAL **: 21:01:31.654: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5140): CRITICAL **: 01:27:03.098: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5140): CRITICAL **: 01:27:03.098: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5140): CRITICAL **: 01:27:03.098: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5016): CRITICAL **: 21:01:32.737: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5016): CRITICAL **: 21:01:32.737: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5016): CRITICAL **: 21:01:32.737: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5144): CRITICAL **: 01:27:04.129: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5144): CRITICAL **: 01:27:04.129: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5144): CRITICAL **: 01:27:04.129: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5019): CRITICAL **: 21:01:33.823: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5019): CRITICAL **: 21:01:33.823: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5019): CRITICAL **: 21:01:33.823: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5147): CRITICAL **: 01:27:05.165: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5147): CRITICAL **: 01:27:05.165: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5147): CRITICAL **: 01:27:05.165: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -126,7 +126,7 @@ on the brain. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 7.777 seconds) + **Total running time of the script:** ( 0 minutes 6.435 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_volume.py: diff --git a/_sources/auto_examples/datasets/plot_volume2D.rst.txt b/_sources/auto_examples/datasets/plot_volume2D.rst.txt index 4eeae0529..80579a828 100644 --- a/_sources/auto_examples/datasets/plot_volume2D.rst.txt +++ b/_sources/auto_examples/datasets/plot_volume2D.rst.txt @@ -78,22 +78,22 @@ used in the last flatmap is .. code-block:: none - /home/runner/work/pycortex/pycortex/cortex/quickflat/utils.py:486: UserWarning: Trying to register the cmap 'RdBu_covar' which already exists. + /home/runner/work/pycortex/pycortex/cortex/quickflat/utils.py:497: UserWarning: Trying to register the cmap 'RdBu_covar' which already exists. cm.register_cmap(dataview.cmap, cmap) Failed to get connection - ** (inkscape:5040): CRITICAL **: 21:01:47.826: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5040): CRITICAL **: 21:01:47.826: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5040): CRITICAL **: 21:01:47.826: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed - /home/runner/work/pycortex/pycortex/cortex/quickflat/utils.py:486: UserWarning: Trying to register the cmap 'RdBu_covar' which already exists. + ** (inkscape:5164): CRITICAL **: 01:27:16.461: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5164): CRITICAL **: 01:27:16.461: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5164): CRITICAL **: 01:27:16.461: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + /home/runner/work/pycortex/pycortex/cortex/quickflat/utils.py:497: UserWarning: Trying to register the cmap 'RdBu_covar' which already exists. cm.register_cmap(dataview.cmap, cmap) Failed to get connection - ** (inkscape:5043): CRITICAL **: 21:01:48.972: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5043): CRITICAL **: 21:01:48.972: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5043): CRITICAL **: 21:01:48.972: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5168): CRITICAL **: 01:27:17.574: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5168): CRITICAL **: 01:27:17.574: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5168): CRITICAL **: 01:27:17.574: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5046): CRITICAL **: 21:01:50.134: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5046): CRITICAL **: 21:01:50.134: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5046): CRITICAL **: 21:01:50.134: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5171): CRITICAL **: 01:27:18.683: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5171): CRITICAL **: 01:27:18.683: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5171): CRITICAL **: 01:27:18.683: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -142,7 +142,7 @@ used in the last flatmap is .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 7.617 seconds) + **Total running time of the script:** ( 0 minutes 6.264 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_volume2D.py: diff --git a/_sources/auto_examples/datasets/plot_volumeRGB.rst.txt b/_sources/auto_examples/datasets/plot_volumeRGB.rst.txt index 030ab221c..930a153e0 100644 --- a/_sources/auto_examples/datasets/plot_volumeRGB.rst.txt +++ b/_sources/auto_examples/datasets/plot_volumeRGB.rst.txt @@ -85,17 +85,17 @@ shared_vmax` will allow you to specify minimum and maximum values manually. .. code-block:: none Failed to get connection - ** (inkscape:5056): CRITICAL **: 21:01:58.240: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5056): CRITICAL **: 21:01:58.240: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5056): CRITICAL **: 21:01:58.240: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5180): CRITICAL **: 01:27:25.026: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5180): CRITICAL **: 01:27:25.026: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5180): CRITICAL **: 01:27:25.026: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5060): CRITICAL **: 21:02:04.739: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5060): CRITICAL **: 21:02:04.739: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5060): CRITICAL **: 21:02:04.739: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5192): CRITICAL **: 01:27:31.612: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5192): CRITICAL **: 01:27:31.612: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5192): CRITICAL **: 01:27:31.612: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5069): CRITICAL **: 21:02:11.284: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5069): CRITICAL **: 21:02:11.284: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5069): CRITICAL **: 21:02:11.284: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5202): CRITICAL **: 01:27:38.226: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5202): CRITICAL **: 01:27:38.227: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5202): CRITICAL **: 01:27:38.227: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -167,7 +167,7 @@ shared_vmax` will allow you to specify minimum and maximum values manually. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 18.246 seconds) + **Total running time of the script:** ( 0 minutes 17.227 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_volumeRGB.py: diff --git a/_sources/auto_examples/datasets/plot_volume_to_vertex.rst.txt b/_sources/auto_examples/datasets/plot_volume_to_vertex.rst.txt index dca15af19..fd1c04e3c 100644 --- a/_sources/auto_examples/datasets/plot_volume_to_vertex.rst.txt +++ b/_sources/auto_examples/datasets/plot_volume_to_vertex.rst.txt @@ -57,14 +57,14 @@ vertex mapping of that data. You can plot both of these as you normally would. .. code-block:: none Failed to get connection - ** (inkscape:5002): CRITICAL **: 21:01:24.992: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5002): CRITICAL **: 21:01:24.992: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5002): CRITICAL **: 21:01:24.992: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5131): CRITICAL **: 01:26:57.515: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5131): CRITICAL **: 01:26:57.515: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5131): CRITICAL **: 01:26:57.515: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Generating a flatmap cache Failed to get connection - ** (inkscape:5007): CRITICAL **: 21:01:27.144: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5007): CRITICAL **: 21:01:27.144: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5007): CRITICAL **: 21:01:27.144: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5134): CRITICAL **: 01:26:59.615: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5134): CRITICAL **: 01:26:59.615: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5134): CRITICAL **: 01:26:59.615: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -104,7 +104,7 @@ vertex mapping of that data. You can plot both of these as you normally would. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 8.172 seconds) + **Total running time of the script:** ( 0 minutes 7.047 seconds) .. _sphx_glr_download_auto_examples_datasets_plot_volume_to_vertex.py: diff --git a/_sources/auto_examples/datasets/sg_execution_times.rst.txt b/_sources/auto_examples/datasets/sg_execution_times.rst.txt index ea0eb7b31..940064ea3 100644 --- a/_sources/auto_examples/datasets/sg_execution_times.rst.txt +++ b/_sources/auto_examples/datasets/sg_execution_times.rst.txt @@ -5,22 +5,22 @@ Computation times ================= -**01:12.319** total execution time for **auto_examples_datasets** files: +**01:03.893** total execution time for **auto_examples_datasets** files: +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_dataset_arithmetic.py` (``plot_dataset_arithmetic.py``) | 00:20.591 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_dataset_arithmetic.py` (``plot_dataset_arithmetic.py``) | 00:18.572 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_volumeRGB.py` (``plot_volumeRGB.py``) | 00:18.246 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_volumeRGB.py` (``plot_volumeRGB.py``) | 00:17.227 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_volume_to_vertex.py` (``plot_volume_to_vertex.py``) | 00:08.172 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_volume_to_vertex.py` (``plot_volume_to_vertex.py``) | 00:07.047 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_volume.py` (``plot_volume.py``) | 00:07.777 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_volume.py` (``plot_volume.py``) | 00:06.435 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_volume2D.py` (``plot_volume2D.py``) | 00:07.617 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_volume2D.py` (``plot_volume2D.py``) | 00:06.264 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_vertex.py` (``plot_vertex.py``) | 00:05.277 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_vertex.py` (``plot_vertex.py``) | 00:04.388 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_vertexRGB.py` (``plot_vertexRGB.py``) | 00:02.322 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_vertexRGB.py` (``plot_vertexRGB.py``) | 00:01.988 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_datasets_plot_vertex2D.py` (``plot_vertex2D.py``) | 00:02.318 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_datasets_plot_vertex2D.py` (``plot_vertex2D.py``) | 00:01.972 | 0.0 MB | +----------------------------------------------------------------------------------------------------+-----------+--------+ diff --git a/_sources/auto_examples/import_surface/import_fmriprep.rst.txt b/_sources/auto_examples/import_surface/import_fmriprep.rst.txt index cd046108a..526a71af8 100644 --- a/_sources/auto_examples/import_surface/import_fmriprep.rst.txt +++ b/_sources/auto_examples/import_surface/import_fmriprep.rst.txt @@ -46,7 +46,7 @@ NB: `cortex.fmriprep` is a work-in-progress and cannot currently handle multiple # import subject into pycortex database fmriprep.import_subj(subject_id, source_directory) - # We can use visualize the imported subject's T1-weighted image + # We can visualize the imported subject's T1-weighted image anat_nifti = 'fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz' t1_image_path = op.join(source_directory, anat_nifti) diff --git a/_sources/auto_examples/index.rst.txt b/_sources/auto_examples/index.rst.txt index 1eb3fc1e8..ea26267f4 100644 --- a/_sources/auto_examples/index.rst.txt +++ b/_sources/auto_examples/index.rst.txt @@ -294,14 +294,14 @@ Examples demonstrating how to create flatmaps. .. raw:: html -
+
.. only:: html - .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_png_thumb.png - :alt: Save a 2D static flatmap as PNG + .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_svg_thumb.png + :alt: Save a 2D static flatmap as SVG - :ref:`sphx_glr_auto_examples_quickflat_plot_make_png.py` + :ref:`sphx_glr_auto_examples_quickflat_plot_make_svg.py` .. raw:: html @@ -311,18 +311,18 @@ Examples demonstrating how to create flatmaps. .. toctree:: :hidden: - /auto_examples/quickflat/plot_make_png + /auto_examples/quickflat/plot_make_svg .. raw:: html -
+
.. only:: html - .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_svg_thumb.png - :alt: Save a 2D static flatmap as SVG + .. figure:: /auto_examples/quickflat/images/thumb/sphx_glr_plot_make_png_thumb.png + :alt: Save a 2D static flatmap as PNG - :ref:`sphx_glr_auto_examples_quickflat_plot_make_svg.py` + :ref:`sphx_glr_auto_examples_quickflat_plot_make_png.py` .. raw:: html @@ -332,7 +332,7 @@ Examples demonstrating how to create flatmaps. .. toctree:: :hidden: - /auto_examples/quickflat/plot_make_svg + /auto_examples/quickflat/plot_make_png .. raw:: html diff --git a/_sources/auto_examples/quickflat/plot_advanced_compositing.rst.txt b/_sources/auto_examples/quickflat/plot_advanced_compositing.rst.txt index 4d38ab3ac..a914b5323 100644 --- a/_sources/auto_examples/quickflat/plot_advanced_compositing.rst.txt +++ b/_sources/auto_examples/quickflat/plot_advanced_compositing.rst.txt @@ -45,17 +45,17 @@ quickflat.composite sub-module. .. code-block:: none Failed to get connection - ** (inkscape:5289): CRITICAL **: 21:06:08.188: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5289): CRITICAL **: 21:06:08.188: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5289): CRITICAL **: 21:06:08.188: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5421): CRITICAL **: 01:31:23.379: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5421): CRITICAL **: 01:31:23.379: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5421): CRITICAL **: 01:31:23.379: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5293): CRITICAL **: 21:06:08.967: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5293): CRITICAL **: 21:06:08.967: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5293): CRITICAL **: 21:06:08.967: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5424): CRITICAL **: 01:31:24.128: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5424): CRITICAL **: 01:31:24.128: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5424): CRITICAL **: 01:31:24.128: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5296): CRITICAL **: 21:06:09.824: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5296): CRITICAL **: 21:06:09.824: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5296): CRITICAL **: 21:06:09.824: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5427): CRITICAL **: 01:31:24.950: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5427): CRITICAL **: 01:31:24.950: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5427): CRITICAL **: 01:31:24.950: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -106,7 +106,7 @@ quickflat.composite sub-module. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 5.655 seconds) + **Total running time of the script:** ( 0 minutes 5.141 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_advanced_compositing.py: diff --git a/_sources/auto_examples/quickflat/plot_connected_vertices.rst.txt b/_sources/auto_examples/quickflat/plot_connected_vertices.rst.txt index 658665a19..ba54c9b66 100644 --- a/_sources/auto_examples/quickflat/plot_connected_vertices.rst.txt +++ b/_sources/auto_examples/quickflat/plot_connected_vertices.rst.txt @@ -46,9 +46,9 @@ connecting lines. Generating a flatmap cache Failed to get connection - ** (inkscape:5135): CRITICAL **: 21:02:58.156: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5135): CRITICAL **: 21:02:58.156: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5135): CRITICAL **: 21:02:58.156: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5268): CRITICAL **: 01:28:18.292: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5268): CRITICAL **: 01:28:18.293: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5268): CRITICAL **: 01:28:18.293: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Shared voxel array not found, generating... Caching mapper... @@ -81,7 +81,7 @@ connecting lines. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 2 minutes 2.031 seconds) + **Total running time of the script:** ( 2 minutes 3.094 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_connected_vertices.py: diff --git a/_sources/auto_examples/quickflat/plot_cutouts.rst.txt b/_sources/auto_examples/quickflat/plot_cutouts.rst.txt index 9e35a27ca..bb838042b 100644 --- a/_sources/auto_examples/quickflat/plot_cutouts.rst.txt +++ b/_sources/auto_examples/quickflat/plot_cutouts.rst.txt @@ -48,13 +48,13 @@ name of the flatmap cutout defined in the `overlays.svg` file. .. code-block:: none Failed to get connection - ** (inkscape:5114): CRITICAL **: 21:02:42.335: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5114): CRITICAL **: 21:02:42.335: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5114): CRITICAL **: 21:02:42.335: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5248): CRITICAL **: 01:28:04.376: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5248): CRITICAL **: 01:28:04.376: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5248): CRITICAL **: 01:28:04.376: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5118): CRITICAL **: 21:02:43.252: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5118): CRITICAL **: 21:02:43.252: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5118): CRITICAL **: 21:02:43.252: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5251): CRITICAL **: 01:28:05.243: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5251): CRITICAL **: 01:28:05.243: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5251): CRITICAL **: 01:28:05.243: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -84,7 +84,7 @@ name of the flatmap cutout defined in the `overlays.svg` file. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 2.161 seconds) + **Total running time of the script:** ( 0 minutes 2.057 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_cutouts.py: diff --git a/_sources/auto_examples/quickflat/plot_dropout.rst.txt b/_sources/auto_examples/quickflat/plot_dropout.rst.txt index 1dea17f38..565c1b2c5 100644 --- a/_sources/auto_examples/quickflat/plot_dropout.rst.txt +++ b/_sources/auto_examples/quickflat/plot_dropout.rst.txt @@ -54,9 +54,9 @@ of this using the following formula: .. code-block:: none Failed to get connection - ** (inkscape:5089): CRITICAL **: 21:02:27.326: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5089): CRITICAL **: 21:02:27.326: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5089): CRITICAL **: 21:02:27.326: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5219): CRITICAL **: 01:27:52.316: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5219): CRITICAL **: 01:27:52.317: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5219): CRITICAL **: 01:27:52.317: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -84,7 +84,7 @@ of this using the following formula: .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 3.716 seconds) + **Total running time of the script:** ( 0 minutes 3.200 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_dropout.py: diff --git a/_sources/auto_examples/quickflat/plot_make_figure.rst.txt b/_sources/auto_examples/quickflat/plot_make_figure.rst.txt index 06bbb907d..bbeaab476 100644 --- a/_sources/auto_examples/quickflat/plot_make_figure.rst.txt +++ b/_sources/auto_examples/quickflat/plot_make_figure.rst.txt @@ -97,25 +97,25 @@ This can be helpful if you think there is no reason that the .. code-block:: none Failed to get connection - ** (inkscape:5267): CRITICAL **: 21:05:54.801: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5267): CRITICAL **: 21:05:54.801: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5267): CRITICAL **: 21:05:54.801: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5402): CRITICAL **: 01:31:11.806: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5402): CRITICAL **: 01:31:11.806: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5402): CRITICAL **: 01:31:11.806: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5271): CRITICAL **: 21:05:55.826: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5271): CRITICAL **: 21:05:55.826: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5271): CRITICAL **: 21:05:55.826: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5406): CRITICAL **: 01:31:12.783: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5406): CRITICAL **: 01:31:12.783: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5406): CRITICAL **: 01:31:12.783: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5274): CRITICAL **: 21:05:56.967: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5274): CRITICAL **: 21:05:56.967: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5274): CRITICAL **: 21:05:56.967: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5409): CRITICAL **: 01:31:13.881: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5409): CRITICAL **: 01:31:13.881: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5409): CRITICAL **: 01:31:13.881: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5277): CRITICAL **: 21:05:58.111: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5277): CRITICAL **: 21:05:58.112: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5277): CRITICAL **: 21:05:58.112: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5412): CRITICAL **: 01:31:14.979: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5412): CRITICAL **: 01:31:14.979: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5412): CRITICAL **: 01:31:14.979: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5280): CRITICAL **: 21:05:59.438: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5280): CRITICAL **: 21:05:59.438: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5280): CRITICAL **: 21:05:59.438: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5415): CRITICAL **: 01:31:16.268: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5415): CRITICAL **: 01:31:16.269: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5415): CRITICAL **: 01:31:16.269: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -172,7 +172,7 @@ This can be helpful if you think there is no reason that the .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 12.942 seconds) + **Total running time of the script:** ( 0 minutes 11.182 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_make_figure.py: diff --git a/_sources/auto_examples/quickflat/plot_make_gif.rst.txt b/_sources/auto_examples/quickflat/plot_make_gif.rst.txt index 116d8e2d5..4cafc0822 100644 --- a/_sources/auto_examples/quickflat/plot_make_gif.rst.txt +++ b/_sources/auto_examples/quickflat/plot_make_gif.rst.txt @@ -105,13 +105,13 @@ Plot flat maps individually .. code-block:: none Failed to get connection - ** (inkscape:5202): CRITICAL **: 21:04:53.516: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5202): CRITICAL **: 21:04:53.516: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5202): CRITICAL **: 21:04:53.516: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5327): CRITICAL **: 01:30:14.896: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5327): CRITICAL **: 01:30:14.896: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5327): CRITICAL **: 01:30:14.896: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5206): CRITICAL **: 21:04:54.583: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5206): CRITICAL **: 21:04:54.583: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5206): CRITICAL **: 21:04:54.583: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5332): CRITICAL **: 01:30:15.933: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5332): CRITICAL **: 01:30:15.933: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5332): CRITICAL **: 01:30:15.933: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -140,13 +140,13 @@ Generate an animated gif that switches between frames every 1.5 seconds .. code-block:: none Failed to get connection - ** (inkscape:5210): CRITICAL **: 21:04:58.842: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5210): CRITICAL **: 21:04:58.842: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5210): CRITICAL **: 21:04:58.842: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5337): CRITICAL **: 01:30:19.261: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5337): CRITICAL **: 01:30:19.261: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5337): CRITICAL **: 01:30:19.262: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5215): CRITICAL **: 21:05:00.824: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5215): CRITICAL **: 21:05:00.824: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5215): CRITICAL **: 21:05:00.824: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5341): CRITICAL **: 01:30:21.048: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5341): CRITICAL **: 01:30:21.049: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5341): CRITICAL **: 01:30:21.049: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -181,13 +181,13 @@ Display gif inline in an IPython notebook .. code-block:: none Failed to get connection - ** (inkscape:5222): CRITICAL **: 21:05:03.707: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5222): CRITICAL **: 21:05:03.707: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5222): CRITICAL **: 21:05:03.707: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5347): CRITICAL **: 01:30:23.595: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5347): CRITICAL **: 01:30:23.595: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5347): CRITICAL **: 01:30:23.595: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5227): CRITICAL **: 21:05:05.703: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5227): CRITICAL **: 21:05:05.703: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5227): CRITICAL **: 21:05:05.703: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5351): CRITICAL **: 01:30:25.381: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5351): CRITICAL **: 01:30:25.381: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5351): CRITICAL **: 01:30:25.381: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -200,7 +200,7 @@ Display gif inline in an IPython notebook .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 14.490 seconds) + **Total running time of the script:** ( 0 minutes 12.570 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_make_gif.py: diff --git a/_sources/auto_examples/quickflat/plot_make_png.rst.txt b/_sources/auto_examples/quickflat/plot_make_png.rst.txt index 131aa40ff..efb68d7be 100644 --- a/_sources/auto_examples/quickflat/plot_make_png.rst.txt +++ b/_sources/auto_examples/quickflat/plot_make_png.rst.txt @@ -54,13 +54,13 @@ that use the parameter `bgcolor`. .. code-block:: none Failed to get connection - ** (inkscape:5094): CRITICAL **: 21:02:30.864: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5094): CRITICAL **: 21:02:30.864: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5094): CRITICAL **: 21:02:30.864: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5233): CRITICAL **: 01:27:59.628: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5233): CRITICAL **: 01:27:59.628: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5233): CRITICAL **: 01:27:59.628: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5097): CRITICAL **: 21:02:31.942: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5097): CRITICAL **: 21:02:31.942: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5097): CRITICAL **: 21:02:31.942: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5238): CRITICAL **: 01:28:00.663: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5238): CRITICAL **: 01:28:00.663: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5238): CRITICAL **: 01:28:00.663: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -90,7 +90,7 @@ that use the parameter `bgcolor`. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 5.443 seconds) + **Total running time of the script:** ( 0 minutes 4.446 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_make_png.py: diff --git a/_sources/auto_examples/quickflat/plot_make_svg.rst.txt b/_sources/auto_examples/quickflat/plot_make_svg.rst.txt index 2eff2ece7..13689d23a 100644 --- a/_sources/auto_examples/quickflat/plot_make_svg.rst.txt +++ b/_sources/auto_examples/quickflat/plot_make_svg.rst.txt @@ -54,13 +54,13 @@ that use the parameter `bgcolor`. .. code-block:: none Failed to get connection - ** (inkscape:5105): CRITICAL **: 21:02:36.567: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5105): CRITICAL **: 21:02:36.567: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5105): CRITICAL **: 21:02:36.567: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5223): CRITICAL **: 01:27:55.257: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5223): CRITICAL **: 01:27:55.257: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5223): CRITICAL **: 01:27:55.257: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5108): CRITICAL **: 21:02:37.638: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5108): CRITICAL **: 21:02:37.638: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5108): CRITICAL **: 21:02:37.638: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5226): CRITICAL **: 01:27:56.295: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5226): CRITICAL **: 01:27:56.295: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5226): CRITICAL **: 01:27:56.295: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -90,7 +90,7 @@ that use the parameter `bgcolor`. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 5.388 seconds) + **Total running time of the script:** ( 0 minutes 4.189 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_make_svg.py: diff --git a/_sources/auto_examples/quickflat/plot_rois.rst.txt b/_sources/auto_examples/quickflat/plot_rois.rst.txt index 1c4bef19f..e02da57df 100644 --- a/_sources/auto_examples/quickflat/plot_rois.rst.txt +++ b/_sources/auto_examples/quickflat/plot_rois.rst.txt @@ -67,13 +67,13 @@ By default, ROIs and ROI labels are displayed when a flatmap is plotted using .. code-block:: none Failed to get connection - ** (inkscape:5122): CRITICAL **: 21:02:44.433: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5122): CRITICAL **: 21:02:44.433: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5122): CRITICAL **: 21:02:44.433: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5256): CRITICAL **: 01:28:06.354: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5256): CRITICAL **: 01:28:06.354: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5256): CRITICAL **: 01:28:06.354: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5126): CRITICAL **: 21:02:45.497: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5126): CRITICAL **: 21:02:45.497: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5126): CRITICAL **: 21:02:45.498: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5260): CRITICAL **: 01:28:07.392: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5260): CRITICAL **: 01:28:07.392: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5260): CRITICAL **: 01:28:07.392: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -108,7 +108,7 @@ By default, ROIs and ROI labels are displayed when a flatmap is plotted using .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 6.585 seconds) + **Total running time of the script:** ( 0 minutes 5.128 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_rois.py: diff --git a/_sources/auto_examples/quickflat/plot_sulci.rst.txt b/_sources/auto_examples/quickflat/plot_sulci.rst.txt index b62f21f63..5a5c9e16f 100644 --- a/_sources/auto_examples/quickflat/plot_sulci.rst.txt +++ b/_sources/auto_examples/quickflat/plot_sulci.rst.txt @@ -45,16 +45,16 @@ displaying the sulci on the surface. .. code-block:: none Generating curvature surface info... - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Failed to get connection - ** (inkscape:5080): CRITICAL **: 21:02:22.382: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5080): CRITICAL **: 21:02:22.382: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5080): CRITICAL **: 21:02:22.382: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5209): CRITICAL **: 01:27:48.014: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5209): CRITICAL **: 01:27:48.014: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5209): CRITICAL **: 01:27:48.014: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5085): CRITICAL **: 21:02:23.300: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5085): CRITICAL **: 21:02:23.300: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5085): CRITICAL **: 21:02:23.300: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5213): CRITICAL **: 01:27:48.884: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5213): CRITICAL **: 01:27:48.884: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5213): CRITICAL **: 01:27:48.884: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -81,7 +81,7 @@ displaying the sulci on the surface. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 9.918 seconds) + **Total running time of the script:** ( 0 minutes 9.313 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_sulci.py: diff --git a/_sources/auto_examples/quickflat/plot_thickness_nanmean.rst.txt b/_sources/auto_examples/quickflat/plot_thickness_nanmean.rst.txt index 1d2c95c88..d9397aa25 100644 --- a/_sources/auto_examples/quickflat/plot_thickness_nanmean.rst.txt +++ b/_sources/auto_examples/quickflat/plot_thickness_nanmean.rst.txt @@ -60,13 +60,13 @@ has the value NaN. .. code-block:: none Failed to get connection - ** (inkscape:5233): CRITICAL **: 21:05:08.391: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5233): CRITICAL **: 21:05:08.391: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5233): CRITICAL **: 21:05:08.391: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5358): CRITICAL **: 01:30:27.787: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5358): CRITICAL **: 01:30:27.787: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5358): CRITICAL **: 01:30:27.787: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5237): CRITICAL **: 21:05:09.610: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5237): CRITICAL **: 21:05:09.610: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5237): CRITICAL **: 21:05:09.610: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5361): CRITICAL **: 01:30:28.963: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5361): CRITICAL **: 01:30:28.963: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5361): CRITICAL **: 01:30:28.963: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -109,7 +109,7 @@ has the value NaN. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 4.873 seconds) + **Total running time of the script:** ( 0 minutes 4.428 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_thickness_nanmean.py: diff --git a/_sources/auto_examples/quickflat/plot_zoom_to_roi.rst.txt b/_sources/auto_examples/quickflat/plot_zoom_to_roi.rst.txt index 39e6fbfb3..d4dbef349 100644 --- a/_sources/auto_examples/quickflat/plot_zoom_to_roi.rst.txt +++ b/_sources/auto_examples/quickflat/plot_zoom_to_roi.rst.txt @@ -55,14 +55,14 @@ show just the region around that ROI. .. code-block:: none Failed to get connection - ** (inkscape:5242): CRITICAL **: 21:05:13.380: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5242): CRITICAL **: 21:05:13.380: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5242): CRITICAL **: 21:05:13.380: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5375): CRITICAL **: 01:30:32.250: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5375): CRITICAL **: 01:30:32.251: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5375): CRITICAL **: 01:30:32.251: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Generating a flatmap cache Failed to get connection - ** (inkscape:5260): CRITICAL **: 21:05:47.674: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5260): CRITICAL **: 21:05:47.674: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5260): CRITICAL **: 21:05:47.674: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5393): CRITICAL **: 01:31:05.967: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5393): CRITICAL **: 01:31:05.967: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5393): CRITICAL **: 01:31:05.967: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -111,7 +111,7 @@ show just the region around that ROI. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 40.946 seconds) + **Total running time of the script:** ( 0 minutes 39.235 seconds) .. _sphx_glr_download_auto_examples_quickflat_plot_zoom_to_roi.py: diff --git a/_sources/auto_examples/quickflat/sg_execution_times.rst.txt b/_sources/auto_examples/quickflat/sg_execution_times.rst.txt index 602f9fc5b..17743c8d8 100644 --- a/_sources/auto_examples/quickflat/sg_execution_times.rst.txt +++ b/_sources/auto_examples/quickflat/sg_execution_times.rst.txt @@ -5,30 +5,30 @@ Computation times ================= -**03:54.148** total execution time for **auto_examples_quickflat** files: +**03:43.983** total execution time for **auto_examples_quickflat** files: +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_connected_vertices.py` (``plot_connected_vertices.py``) | 02:02.031 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_connected_vertices.py` (``plot_connected_vertices.py``) | 02:03.094 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_zoom_to_roi.py` (``plot_zoom_to_roi.py``) | 00:40.946 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_zoom_to_roi.py` (``plot_zoom_to_roi.py``) | 00:39.235 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_make_gif.py` (``plot_make_gif.py``) | 00:14.490 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_make_gif.py` (``plot_make_gif.py``) | 00:12.570 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_make_figure.py` (``plot_make_figure.py``) | 00:12.942 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_make_figure.py` (``plot_make_figure.py``) | 00:11.182 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_sulci.py` (``plot_sulci.py``) | 00:09.918 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_sulci.py` (``plot_sulci.py``) | 00:09.313 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_rois.py` (``plot_rois.py``) | 00:06.585 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_advanced_compositing.py` (``plot_advanced_compositing.py``) | 00:05.141 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_advanced_compositing.py` (``plot_advanced_compositing.py``) | 00:05.655 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_rois.py` (``plot_rois.py``) | 00:05.128 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_make_png.py` (``plot_make_png.py``) | 00:05.443 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_make_png.py` (``plot_make_png.py``) | 00:04.446 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_make_svg.py` (``plot_make_svg.py``) | 00:05.388 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_thickness_nanmean.py` (``plot_thickness_nanmean.py``) | 00:04.428 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_thickness_nanmean.py` (``plot_thickness_nanmean.py``) | 00:04.873 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_make_svg.py` (``plot_make_svg.py``) | 00:04.189 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_dropout.py` (``plot_dropout.py``) | 00:03.716 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_dropout.py` (``plot_dropout.py``) | 00:03.200 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickflat_plot_cutouts.py` (``plot_cutouts.py``) | 00:02.161 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickflat_plot_cutouts.py` (``plot_cutouts.py``) | 00:02.057 | 0.0 MB | +---------------------------------------------------------------------------------------------------------+-----------+--------+ diff --git a/_sources/auto_examples/quickstart/plot_retinotopy_flatmap.rst.txt b/_sources/auto_examples/quickstart/plot_retinotopy_flatmap.rst.txt index 7753bcedc..564192d45 100644 --- a/_sources/auto_examples/quickstart/plot_retinotopy_flatmap.rst.txt +++ b/_sources/auto_examples/quickstart/plot_retinotopy_flatmap.rst.txt @@ -64,13 +64,13 @@ and you will also need a flatmap for them. Mask not found, generating... Failed to get connection - ** (inkscape:5302): CRITICAL **: 21:06:15.981: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5302): CRITICAL **: 21:06:15.981: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5302): CRITICAL **: 21:06:15.981: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5434): CRITICAL **: 01:31:30.199: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5434): CRITICAL **: 01:31:30.199: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5434): CRITICAL **: 01:31:30.200: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5305): CRITICAL **: 21:06:17.138: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5305): CRITICAL **: 21:06:17.138: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5305): CRITICAL **: 21:06:17.138: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5438): CRITICAL **: 01:31:31.326: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5438): CRITICAL **: 01:31:31.326: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5438): CRITICAL **: 01:31:31.326: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -113,7 +113,7 @@ and you will also need a flatmap for them. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 7.138 seconds) + **Total running time of the script:** ( 0 minutes 6.018 seconds) .. _sphx_glr_download_auto_examples_quickstart_plot_retinotopy_flatmap.py: diff --git a/_sources/auto_examples/quickstart/sg_execution_times.rst.txt b/_sources/auto_examples/quickstart/sg_execution_times.rst.txt index 92fb0bdab..cf25927b0 100644 --- a/_sources/auto_examples/quickstart/sg_execution_times.rst.txt +++ b/_sources/auto_examples/quickstart/sg_execution_times.rst.txt @@ -5,10 +5,10 @@ Computation times ================= -**00:07.138** total execution time for **auto_examples_quickstart** files: +**00:06.018** total execution time for **auto_examples_quickstart** files: +------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_quickstart_plot_retinotopy_flatmap.py` (``plot_retinotopy_flatmap.py``) | 00:07.138 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_quickstart_plot_retinotopy_flatmap.py` (``plot_retinotopy_flatmap.py``) | 00:06.018 | 0.0 MB | +------------------------------------------------------------------------------------------------------+-----------+--------+ | :ref:`sphx_glr_auto_examples_quickstart_retinotopy_webgl.py` (``retinotopy_webgl.py``) | 00:00.000 | 0.0 MB | +------------------------------------------------------------------------------------------------------+-----------+--------+ diff --git a/_sources/auto_examples/surface_analyses/plot_flatmap_distortion.rst.txt b/_sources/auto_examples/surface_analyses/plot_flatmap_distortion.rst.txt index b704e1ce1..aa7e8ada9 100644 --- a/_sources/auto_examples/surface_analyses/plot_flatmap_distortion.rst.txt +++ b/_sources/auto_examples/surface_analyses/plot_flatmap_distortion.rst.txt @@ -71,11 +71,11 @@ the original. Generating distortion surface info... /home/runner/work/pycortex/pycortex/cortex/polyutils/distortion.py:57: RuntimeWarning: invalid value encountered in true_divide vertratios /= np.bincount(self.polys.ravel(), minlength=len(self.ref)) - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) /home/runner/work/pycortex/pycortex/cortex/polyutils/distortion.py:57: RuntimeWarning: invalid value encountered in true_divide vertratios /= np.bincount(self.polys.ravel(), minlength=len(self.ref)) - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Generating distortion surface info... @@ -136,7 +136,7 @@ the original. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 31.399 seconds) + **Total running time of the script:** ( 0 minutes 30.161 seconds) .. _sphx_glr_download_auto_examples_surface_analyses_plot_flatmap_distortion.py: diff --git a/_sources/auto_examples/surface_analyses/plot_geodesic_distance.rst.txt b/_sources/auto_examples/surface_analyses/plot_geodesic_distance.rst.txt index e899ff0db..acf90a75b 100644 --- a/_sources/auto_examples/surface_analyses/plot_geodesic_distance.rst.txt +++ b/_sources/auto_examples/surface_analyses/plot_geodesic_distance.rst.txt @@ -62,16 +62,16 @@ The two hemispheres must be run separately. .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Failed to get connection - ** (inkscape:5341): CRITICAL **: 21:07:15.431: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5341): CRITICAL **: 21:07:15.431: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5341): CRITICAL **: 21:07:15.432: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5473): CRITICAL **: 01:32:28.085: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5473): CRITICAL **: 01:32:28.085: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5473): CRITICAL **: 01:32:28.085: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5345): CRITICAL **: 21:07:17.236: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5345): CRITICAL **: 21:07:17.236: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5345): CRITICAL **: 21:07:17.236: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5477): CRITICAL **: 01:32:29.814: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5477): CRITICAL **: 01:32:29.814: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5477): CRITICAL **: 01:32:29.814: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -124,7 +124,7 @@ The two hemispheres must be run separately. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 15.731 seconds) + **Total running time of the script:** ( 0 minutes 14.953 seconds) .. _sphx_glr_download_auto_examples_surface_analyses_plot_geodesic_distance.py: diff --git a/_sources/auto_examples/surface_analyses/plot_geodesic_path.rst.txt b/_sources/auto_examples/surface_analyses/plot_geodesic_path.rst.txt index b68bbdc3f..27bae8682 100644 --- a/_sources/auto_examples/surface_analyses/plot_geodesic_path.rst.txt +++ b/_sources/auto_examples/surface_analyses/plot_geodesic_path.rst.txt @@ -48,12 +48,12 @@ show all of the vertices listed in the path. .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Failed to get connection - ** (inkscape:5332): CRITICAL **: 21:07:02.715: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5332): CRITICAL **: 21:07:02.715: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5332): CRITICAL **: 21:07:02.715: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5462): CRITICAL **: 01:32:15.597: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5462): CRITICAL **: 01:32:15.597: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5462): CRITICAL **: 01:32:15.597: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -97,7 +97,7 @@ show all of the vertices listed in the path. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 9.131 seconds) + **Total running time of the script:** ( 0 minutes 8.814 seconds) .. _sphx_glr_download_auto_examples_surface_analyses_plot_geodesic_path.py: diff --git a/_sources/auto_examples/surface_analyses/plot_interpolate_data.rst.txt b/_sources/auto_examples/surface_analyses/plot_interpolate_data.rst.txt index a61c78dad..2c5c9e34e 100644 --- a/_sources/auto_examples/surface_analyses/plot_interpolate_data.rst.txt +++ b/_sources/auto_examples/surface_analyses/plot_interpolate_data.rst.txt @@ -45,7 +45,7 @@ the selected points. This is similar to thin plate splines. .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) @@ -109,7 +109,7 @@ the selected points. This is similar to thin plate splines. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 16.019 seconds) + **Total running time of the script:** ( 0 minutes 15.640 seconds) .. _sphx_glr_download_auto_examples_surface_analyses_plot_interpolate_data.py: diff --git a/_sources/auto_examples/surface_analyses/plot_subsurfaces.rst.txt b/_sources/auto_examples/surface_analyses/plot_subsurfaces.rst.txt index a0dbd643e..829f54623 100644 --- a/_sources/auto_examples/surface_analyses/plot_subsurfaces.rst.txt +++ b/_sources/auto_examples/surface_analyses/plot_subsurfaces.rst.txt @@ -75,7 +75,7 @@ create subsurface .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) @@ -111,12 +111,12 @@ plot data on subsurface .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Failed to get connection - ** (inkscape:5362): CRITICAL **: 21:07:52.659: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5362): CRITICAL **: 21:07:52.659: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5362): CRITICAL **: 21:07:52.659: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5499): CRITICAL **: 01:33:03.252: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5499): CRITICAL **: 01:33:03.252: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5499): CRITICAL **: 01:33:03.252: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -189,12 +189,12 @@ create many patches .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Failed to get connection - ** (inkscape:5368): CRITICAL **: 21:07:59.079: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5368): CRITICAL **: 21:07:59.079: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5368): CRITICAL **: 21:07:59.079: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5506): CRITICAL **: 01:33:09.549: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5506): CRITICAL **: 01:33:09.549: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5506): CRITICAL **: 01:33:09.549: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -258,20 +258,20 @@ create geodesic strip patch .. code-block:: none - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Failed to get connection - ** (inkscape:5379): CRITICAL **: 21:08:10.358: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5379): CRITICAL **: 21:08:10.358: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5379): CRITICAL **: 21:08:10.358: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5514): CRITICAL **: 01:33:20.494: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5514): CRITICAL **: 01:33:20.494: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5514): CRITICAL **: 01:33:20.494: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5382): CRITICAL **: 21:08:11.387: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5382): CRITICAL **: 21:08:11.387: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5382): CRITICAL **: 21:08:11.387: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5517): CRITICAL **: 01:33:21.485: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5517): CRITICAL **: 01:33:21.485: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5517): CRITICAL **: 01:33:21.486: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Failed to get connection - ** (inkscape:5385): CRITICAL **: 21:08:12.407: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5385): CRITICAL **: 21:08:12.407: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5385): CRITICAL **: 21:08:12.407: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5520): CRITICAL **: 01:33:22.471: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5520): CRITICAL **: 01:33:22.471: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5520): CRITICAL **: 01:33:22.471: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -279,7 +279,7 @@ create geodesic strip patch .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 23.834 seconds) + **Total running time of the script:** ( 0 minutes 22.744 seconds) .. _sphx_glr_download_auto_examples_surface_analyses_plot_subsurfaces.py: diff --git a/_sources/auto_examples/surface_analyses/plot_tissots_indicatrix.rst.txt b/_sources/auto_examples/surface_analyses/plot_tissots_indicatrix.rst.txt index 6cfcefc6f..3449963e6 100644 --- a/_sources/auto_examples/surface_analyses/plot_tissots_indicatrix.rst.txt +++ b/_sources/auto_examples/surface_analyses/plot_tissots_indicatrix.rst.txt @@ -58,7 +58,7 @@ introduced by flattening the globe onto a map: .. code-block:: none Generating tissots_indicatrix surface info... - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Adding vertex 88060.. Adding vertex 93467.. @@ -209,7 +209,7 @@ introduced by flattening the globe onto a map: Adding vertex 6044.. Adding vertex 67298.. Adding vertex 40064.. - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/numpy/lib/npyio.py:713: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/numpy/lib/npyio.py:713: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. val = np.asanyarray(val) @@ -234,7 +234,7 @@ introduced by flattening the globe onto a map: .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 34.081 seconds) + **Total running time of the script:** ( 0 minutes 33.731 seconds) .. _sphx_glr_download_auto_examples_surface_analyses_plot_tissots_indicatrix.py: diff --git a/_sources/auto_examples/surface_analyses/sg_execution_times.rst.txt b/_sources/auto_examples/surface_analyses/sg_execution_times.rst.txt index cece798ae..38cdd114a 100644 --- a/_sources/auto_examples/surface_analyses/sg_execution_times.rst.txt +++ b/_sources/auto_examples/surface_analyses/sg_execution_times.rst.txt @@ -5,18 +5,18 @@ Computation times ================= -**02:10.194** total execution time for **auto_examples_surface_analyses** files: +**02:06.044** total execution time for **auto_examples_surface_analyses** files: +------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_surface_analyses_plot_tissots_indicatrix.py` (``plot_tissots_indicatrix.py``) | 00:34.081 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_surface_analyses_plot_tissots_indicatrix.py` (``plot_tissots_indicatrix.py``) | 00:33.731 | 0.0 MB | +------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_surface_analyses_plot_flatmap_distortion.py` (``plot_flatmap_distortion.py``) | 00:31.399 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_surface_analyses_plot_flatmap_distortion.py` (``plot_flatmap_distortion.py``) | 00:30.161 | 0.0 MB | +------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_surface_analyses_plot_subsurfaces.py` (``plot_subsurfaces.py``) | 00:23.834 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_surface_analyses_plot_subsurfaces.py` (``plot_subsurfaces.py``) | 00:22.744 | 0.0 MB | +------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_surface_analyses_plot_interpolate_data.py` (``plot_interpolate_data.py``) | 00:16.019 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_surface_analyses_plot_interpolate_data.py` (``plot_interpolate_data.py``) | 00:15.640 | 0.0 MB | +------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_distance.py` (``plot_geodesic_distance.py``) | 00:15.731 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_distance.py` (``plot_geodesic_distance.py``) | 00:14.953 | 0.0 MB | +------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_path.py` (``plot_geodesic_path.py``) | 00:09.131 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_surface_analyses_plot_geodesic_path.py` (``plot_geodesic_path.py``) | 00:08.814 | 0.0 MB | +------------------------------------------------------------------------------------------------------------+-----------+--------+ diff --git a/_sources/auto_examples/utils/plot_get_roi_vertices.rst.txt b/_sources/auto_examples/utils/plot_get_roi_vertices.rst.txt index 15761c36d..01bc61459 100644 --- a/_sources/auto_examples/utils/plot_get_roi_vertices.rst.txt +++ b/_sources/auto_examples/utils/plot_get_roi_vertices.rst.txt @@ -42,9 +42,9 @@ defined in the SVG ROI file (see :doc:`/rois.rst`). .. code-block:: none Failed to get connection - ** (inkscape:5395): CRITICAL **: 21:08:33.300: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5395): CRITICAL **: 21:08:33.300: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5395): CRITICAL **: 21:08:33.300: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5534): CRITICAL **: 01:33:42.301: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5534): CRITICAL **: 01:33:42.301: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5534): CRITICAL **: 01:33:42.301: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
@@ -75,7 +75,7 @@ defined in the SVG ROI file (see :doc:`/rois.rst`). .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 2.482 seconds) + **Total running time of the script:** ( 0 minutes 2.277 seconds) .. _sphx_glr_download_auto_examples_utils_plot_get_roi_vertices.py: diff --git a/_sources/auto_examples/utils/plot_mosaic.rst.txt b/_sources/auto_examples/utils/plot_mosaic.rst.txt index caeed540d..ecab1d109 100644 --- a/_sources/auto_examples/utils/plot_mosaic.rst.txt +++ b/_sources/auto_examples/utils/plot_mosaic.rst.txt @@ -104,7 +104,7 @@ The function `mosaic` plots all of the slices in a volume in a matplotlib figure .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 0.414 seconds) + **Total running time of the script:** ( 0 minutes 0.272 seconds) .. _sphx_glr_download_auto_examples_utils_plot_mosaic.py: diff --git a/_sources/auto_examples/utils/plot_roi_voxel_index_volume.rst.txt b/_sources/auto_examples/utils/plot_roi_voxel_index_volume.rst.txt index 6ab79c0a5..dcac0aa38 100644 --- a/_sources/auto_examples/utils/plot_roi_voxel_index_volume.rst.txt +++ b/_sources/auto_examples/utils/plot_roi_voxel_index_volume.rst.txt @@ -42,27 +42,27 @@ ROIs in the right hemisphere will have positive values. .. code-block:: none - /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:487: UserWarning: Requested layer in svg file (V3A) contains no splines + /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:491: UserWarning: Requested layer in svg file (V3A) contains no splines warnings.warn("Requested layer in svg file (%s) contains no splines"%self.name) /home/runner/work/pycortex/pycortex/cortex/utils.py:335: UserWarning: No vertices found in V3A! warnings.warn("No vertices found in {}!".format(name)) - /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:487: UserWarning: Requested layer in svg file (V3B) contains no splines + /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:491: UserWarning: Requested layer in svg file (V3B) contains no splines warnings.warn("Requested layer in svg file (%s) contains no splines"%self.name) /home/runner/work/pycortex/pycortex/cortex/utils.py:335: UserWarning: No vertices found in V3B! warnings.warn("No vertices found in {}!".format(name)) - /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:487: UserWarning: Requested layer in svg file (LO) contains no splines + /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:491: UserWarning: Requested layer in svg file (LO) contains no splines warnings.warn("Requested layer in svg file (%s) contains no splines"%self.name) /home/runner/work/pycortex/pycortex/cortex/utils.py:335: UserWarning: No vertices found in LO! warnings.warn("No vertices found in {}!".format(name)) - /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:487: UserWarning: Requested layer in svg file (V4) contains no splines + /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:491: UserWarning: Requested layer in svg file (V4) contains no splines warnings.warn("Requested layer in svg file (%s) contains no splines"%self.name) /home/runner/work/pycortex/pycortex/cortex/utils.py:335: UserWarning: No vertices found in V4! warnings.warn("No vertices found in {}!".format(name)) - /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:487: UserWarning: Requested layer in svg file (V7) contains no splines + /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:491: UserWarning: Requested layer in svg file (V7) contains no splines warnings.warn("Requested layer in svg file (%s) contains no splines"%self.name) /home/runner/work/pycortex/pycortex/cortex/utils.py:335: UserWarning: No vertices found in V7! warnings.warn("No vertices found in {}!".format(name)) - /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:487: UserWarning: Requested layer in svg file (IFSFP) contains no splines + /home/runner/work/pycortex/pycortex/cortex/svgoverlay.py:491: UserWarning: Requested layer in svg file (IFSFP) contains no splines warnings.warn("Requested layer in svg file (%s) contains no splines"%self.name) /home/runner/work/pycortex/pycortex/cortex/utils.py:335: UserWarning: No vertices found in IFSFP! warnings.warn("No vertices found in {}!".format(name)) @@ -77,7 +77,7 @@ ROIs in the right hemisphere will have positive values. Found 100.00% of M1M /home/runner/work/pycortex/pycortex/cortex/utils.py:621: RuntimeWarning: Mean of empty slice. pct_coverage[roi] = vert_in_scan.mean() * 100 - /opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars + /opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) Found nan% of V3A Found nan% of V3B @@ -104,9 +104,9 @@ ROIs in the right hemisphere will have positive values. Found 100.00% of FFA Cutting 0 overlapping voxels (should be < ~50) Failed to get connection - ** (inkscape:5419): CRITICAL **: 21:08:56.537: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5419): CRITICAL **: 21:08:56.537: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5419): CRITICAL **: 21:08:56.537: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5552): CRITICAL **: 01:34:04.502: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5552): CRITICAL **: 01:34:04.502: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5552): CRITICAL **: 01:34:04.502: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed Index keys for which ROI is which in `index_volume`: {'S1H': 1, 'S1M': 2, 'sPMv': 3, 'PMvh': 4, 'M1F': 5, 'M1H': 6, 'Broca': 7, 'SMFA': 8, 'M1M': 9, 'V3A': 10, 'V3B': 11, 'FO': 12, 'PPA': 13, 'S2F': 14, 'SEF': 15, 'LO': 16, 'V1': 17, 'V2': 18, 'V3': 19, 'V4': 20, 'V7': 21, 'FEF': 22, 'AC': 23, 'OFA': 24, 'IFSFP': 25, 'S1F': 26, 'OPA': 27, 'EBA': 28, 'RSC': 29, 'IPS': 30, 'SMHA': 31, 'FFA': 32} @@ -157,7 +157,7 @@ ROIs in the right hemisphere will have positive values. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 10.143 seconds) + **Total running time of the script:** ( 0 minutes 9.884 seconds) .. _sphx_glr_download_auto_examples_utils_plot_roi_voxel_index_volume.py: diff --git a/_sources/auto_examples/utils/plot_roi_voxel_mask.rst.txt b/_sources/auto_examples/utils/plot_roi_voxel_mask.rst.txt index 456efbf3f..38ec1dc7b 100644 --- a/_sources/auto_examples/utils/plot_roi_voxel_mask.rst.txt +++ b/_sources/auto_examples/utils/plot_roi_voxel_mask.rst.txt @@ -50,9 +50,9 @@ overlays.svg file in the pycortex filestore for this subject. Cutting 0 overlapping voxels (should be < ~50) Generating a flatmap cache Failed to get connection - ** (inkscape:5409): CRITICAL **: 21:08:46.199: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed - ** (inkscape:5409): CRITICAL **: 21:08:46.199: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed - ** (inkscape:5409): CRITICAL **: 21:08:46.199: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed + ** (inkscape:5543): CRITICAL **: 01:33:54.463: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed + ** (inkscape:5543): CRITICAL **: 01:33:54.463: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed + ** (inkscape:5543): CRITICAL **: 01:33:54.464: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed @@ -98,7 +98,7 @@ overlays.svg file in the pycortex filestore for this subject. .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 7.768 seconds) + **Total running time of the script:** ( 0 minutes 7.399 seconds) .. _sphx_glr_download_auto_examples_utils_plot_roi_voxel_mask.py: diff --git a/_sources/auto_examples/utils/plot_voxel_distance_from_surface.rst.txt b/_sources/auto_examples/utils/plot_voxel_distance_from_surface.rst.txt index e8a3e2b21..265a631b1 100644 --- a/_sources/auto_examples/utils/plot_voxel_distance_from_surface.rst.txt +++ b/_sources/auto_examples/utils/plot_voxel_distance_from_surface.rst.txt @@ -41,7 +41,7 @@ The utility function `get_vox_dist` returns the distance from each voxel in some .. code-block:: none - + @@ -73,7 +73,7 @@ The utility function `get_vox_dist` returns the distance from each voxel in some .. rst-class:: sphx-glr-timing - **Total running time of the script:** ( 0 minutes 4.422 seconds) + **Total running time of the script:** ( 0 minutes 4.326 seconds) .. _sphx_glr_download_auto_examples_utils_plot_voxel_distance_from_surface.py: diff --git a/_sources/auto_examples/utils/sg_execution_times.rst.txt b/_sources/auto_examples/utils/sg_execution_times.rst.txt index da945aebb..720ada408 100644 --- a/_sources/auto_examples/utils/sg_execution_times.rst.txt +++ b/_sources/auto_examples/utils/sg_execution_times.rst.txt @@ -5,18 +5,18 @@ Computation times ================= -**00:25.229** total execution time for **auto_examples_utils** files: +**00:24.158** total execution time for **auto_examples_utils** files: +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_index_volume.py` (``plot_roi_voxel_index_volume.py``) | 00:10.143 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_index_volume.py` (``plot_roi_voxel_index_volume.py``) | 00:09.884 | 0.0 MB | +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_mask.py` (``plot_roi_voxel_mask.py``) | 00:07.768 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_utils_plot_roi_voxel_mask.py` (``plot_roi_voxel_mask.py``) | 00:07.399 | 0.0 MB | +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_utils_plot_voxel_distance_from_surface.py` (``plot_voxel_distance_from_surface.py``) | 00:04.422 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_utils_plot_voxel_distance_from_surface.py` (``plot_voxel_distance_from_surface.py``) | 00:04.326 | 0.0 MB | +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_utils_plot_get_roi_vertices.py` (``plot_get_roi_vertices.py``) | 00:02.482 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_utils_plot_get_roi_vertices.py` (``plot_get_roi_vertices.py``) | 00:02.277 | 0.0 MB | +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr_auto_examples_utils_plot_mosaic.py` (``plot_mosaic.py``) | 00:00.414 | 0.0 MB | +| :ref:`sphx_glr_auto_examples_utils_plot_mosaic.py` (``plot_mosaic.py``) | 00:00.272 | 0.0 MB | +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ | :ref:`sphx_glr_auto_examples_utils_mni_to_subject.py` (``mni_to_subject.py``) | 00:00.000 | 0.0 MB | +-------------------------------------------------------------------------------------------------------------------+-----------+--------+ diff --git a/_static/doctools.js b/_static/doctools.js index e509e4834..e1bfd708b 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -154,9 +154,7 @@ var Documentation = { this.fixFirefoxAnchorBug(); this.highlightSearchWords(); this.initIndexTable(); - if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { - this.initOnKeyListeners(); - } + this.initOnKeyListeners(); }, /** @@ -269,6 +267,13 @@ var Documentation = { window.history.replaceState({}, '', url); }, + /** + * helper function to focus on search bar + */ + focusSearchBar : function() { + $('input[name=q]').first().focus(); + }, + /** * make the url absolute */ @@ -291,27 +296,54 @@ var Documentation = { }, initOnKeyListeners: function() { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) + return; + $(document).keydown(function(event) { var activeElementType = document.activeElement.tagName; // don't navigate when in search box, textarea, dropdown or button if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT' - && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey - && !event.shiftKey) { - switch (event.keyCode) { - case 37: // left - var prevHref = $('link[rel="prev"]').prop('href'); - if (prevHref) { - window.location.href = prevHref; - return false; - } - break; - case 39: // right - var nextHref = $('link[rel="next"]').prop('href'); - if (nextHref) { - window.location.href = nextHref; - return false; - } - break; + && activeElementType !== 'BUTTON') { + if (event.altKey || event.ctrlKey || event.metaKey) + return; + + if (!event.shiftKey) { + switch (event.key) { + case 'ArrowLeft': + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) + break; + var prevHref = $('link[rel="prev"]').prop('href'); + if (prevHref) { + window.location.href = prevHref; + return false; + } + break; + case 'ArrowRight': + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) + break; + var nextHref = $('link[rel="next"]').prop('href'); + if (nextHref) { + window.location.href = nextHref; + return false; + } + break; + case 'Escape': + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) + break; + Documentation.hideSearchWords(); + return false; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case '/': + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) + break; + Documentation.focusSearchBar(); + return false; } } }); diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 5dfebe0ae..62e970da4 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.2.3', + VERSION: '1.2.4', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', @@ -8,5 +8,7 @@ var DOCUMENTATION_OPTIONS = { LINK_SUFFIX: '.html', HAS_SOURCE: true, SOURCELINK_SUFFIX: '.txt', - NAVIGATION_WITH_KEYS: false + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, }; \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js index 2d7785937..0a44e8582 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -172,10 +172,6 @@ var Search = { } // stem the word var word = stemmer.stemWord(tmp[i].toLowerCase()); - // prevent stemmer from cutting word smaller than two chars - if(word.length < 3 && tmp[i].length >= 3) { - word = tmp[i]; - } var toAppend; // select the correct list if (word[0] == '-') { @@ -276,7 +272,7 @@ var Search = { setTimeout(function() { displayNextItem(); }, 5); - } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { + } else if (DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY) { $.ajax({url: requestUrl, dataType: "text", complete: function(jqxhr, textstatus) { @@ -293,7 +289,7 @@ var Search = { }, 5); }}); } else { - // no source available, just display title + // just display title Search.output.append(listItem); setTimeout(function() { displayNextItem(); diff --git a/align.html b/align.html index d6cef30c3..2047ce7ec 100644 --- a/align.html +++ b/align.html @@ -6,7 +6,7 @@ - Alignments — pycortex 1.2.3 documentation + Alignments — pycortex 1.2.4 documentation @@ -232,7 +232,7 @@

Quick search

©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/api_reference_flat.html b/api_reference_flat.html index ff6462aa2..e25a7ccc9 100644 --- a/api_reference_flat.html +++ b/api_reference_flat.html @@ -6,7 +6,7 @@ - Python API Reference — pycortex 1.2.3 documentation + Python API Reference — pycortex 1.2.4 documentation @@ -70,7 +70,7 @@

Most commonly used modules

quickflat

- +
@@ -91,7 +91,7 @@

Most commonly used modules

webgl

Makes an interactive viewer for viewing data in a browser

-

+
@@ -109,7 +109,7 @@

Most commonly used modules

dataset

Contains classes for representing brain data in either volumetric or vertex (surface-based) formats for visualization.

-

+
@@ -145,14 +145,14 @@

All the other modules

align

Contains functions for making alignments between functional data and the surface, or, finding where the brain is.

-

+
- - + + @@ -166,7 +166,7 @@

All the other modules

anat

Contains functions for making a whitematter mask

-

manual(subject, xfmname[, reference])

Open GUI for manually aligning a functional volume to the cortical surface for subject.

manual(subject, xfmname[, output_name, ...])

Open Freesurfer FreeView GUI for manually aligning/adjusting a functional volume to the cortical surface for subject.

automatic(subject, xfmname, reference[, ...])

Create an automatic alignment using the FLIRT boundary-based alignment (BBR) from FSL.

+
@@ -187,7 +187,7 @@

All the other modules

database

Contains a singleton object db of type Database which allows easy access to surface files, anatomical images, and transforms that are stored in the pycortex filestore.

-

+
@@ -202,7 +202,7 @@

All the other modules

freesurfer

Contains functions for interfacing with freesurfer

-

+
@@ -264,7 +264,7 @@

All the other modules

mapper

-

+
@@ -283,7 +283,7 @@

All the other modules

mni

Functions for finding MNI transforms for individual subjects and transforming functional data and surfaces to and from MNI space.

-

+
@@ -306,7 +306,7 @@

All the other modules

polyutils

-

+
@@ -324,7 +324,7 @@

All the other modules

segment

Controls functions for segmentation of white/gray matter and other things in the brain.

-

+
@@ -349,7 +349,7 @@

All the other modules

surfinfo

Contains functions for computing various surface properties. Mostly wrappers for functions in polyutils.Surface and polyutils.Distortion.

-

+
@@ -376,7 +376,7 @@

All the other modules

utils

Contain utility functions

-

+
@@ -441,7 +441,7 @@

All the other modules

volume

Contains functions for working with volume data

-

+
@@ -480,7 +480,7 @@

All the other modules

xfm

Affine transformation class

-

+
@@ -592,7 +592,7 @@

Quick search

©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/datasets/plot_dataset_arithmetic.html b/auto_examples/datasets/plot_dataset_arithmetic.html index 7a9d044fc..bf7a40d37 100644 --- a/auto_examples/datasets/plot_dataset_arithmetic.html +++ b/auto_examples/datasets/plot_dataset_arithmetic.html @@ -6,7 +6,7 @@ - Dataset Arithmetic — pycortex 1.2.3 documentation + Dataset Arithmetic — pycortex 1.2.4 documentation @@ -57,17 +57,17 @@

Out:

Generating a flatmap cache
 Failed to get connection
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 Failed to get connection
-** (inkscape:4990): CRITICAL **: 21:01:16.307: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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+** (inkscape:5119): CRITICAL **: 01:26:50.304: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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+** (inkscape:5119): CRITICAL **: 01:26:50.304: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
 Failed to get connection
-** (inkscape:4994): CRITICAL **: 21:01:17.382: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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-** (inkscape:4994): CRITICAL **: 21:01:17.382: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
+** (inkscape:5122): CRITICAL **: 01:26:51.342: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
+** (inkscape:5122): CRITICAL **: 01:26:51.342: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
+** (inkscape:5122): CRITICAL **: 01:26:51.342: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
 
@@ -102,7 +102,7 @@ plt.show()
-

Total running time of the script: ( 0 minutes 20.591 seconds)

+

Total running time of the script: ( 0 minutes 18.572 seconds)

@@ -46,35 +46,35 @@ - + - + - + - + - + - + - + - + @@ -154,7 +154,7 @@

Quick search

©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/import_surface/import_fmriprep.html b/auto_examples/import_surface/import_fmriprep.html index 8c37f2c4d..1834f02fd 100644 --- a/auto_examples/import_surface/import_fmriprep.html +++ b/auto_examples/import_surface/import_fmriprep.html @@ -6,7 +6,7 @@ - Import fmriprep output — pycortex 1.2.3 documentation + Import fmriprep output — pycortex 1.2.4 documentation @@ -60,7 +60,7 @@ # import subject into pycortex databasefmriprep.import_subj(subject_id,source_directory) -# We can use visualize the imported subject's T1-weighted image +# We can visualize the imported subject's T1-weighted imageanat_nifti='fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz't1_image_path=op.join(source_directory,anat_nifti) @@ -173,7 +173,7 @@

Quick search

©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/index.html b/auto_examples/index.html index 46e5404fe..9f12d1a88 100644 --- a/auto_examples/index.html +++ b/auto_examples/index.html @@ -6,7 +6,7 @@ - Example Gallery — pycortex 1.2.3 documentation + Example Gallery — pycortex 1.2.4 documentation @@ -151,18 +151,18 @@
-
-Save a 2D static flatmap as PNG +
-
-Save a 2D static flatmap as SVG +
@@ -488,8 +488,8 @@

Navigation

  • Quickflat Examples
    • Plot sulci on the flatmap
    • Plot dropout regions on the flatmap
    • -
    • Save a 2D static flatmap as PNG
    • Save a 2D static flatmap as SVG
    • +
    • Save a 2D static flatmap as PNG
    • Plot cutouts on the flatmap
    • Plot ROIs on the flatmap
    • Plot which vertices are inside the same voxels
    • @@ -576,7 +576,7 @@

      Quick search

      ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/quickflat/plot_advanced_compositing.html b/auto_examples/quickflat/plot_advanced_compositing.html index b1b812b3c..1a77c2f31 100644 --- a/auto_examples/quickflat/plot_advanced_compositing.html +++ b/auto_examples/quickflat/plot_advanced_compositing.html @@ -6,7 +6,7 @@ - Plot with advanced compositing — pycortex 1.2.3 documentation + Plot with advanced compositing — pycortex 1.2.4 documentation @@ -51,17 +51,17 @@ quickflat.composite sub-module.

      plot advanced compositing

      Out:

      Failed to get connection
      -** (inkscape:5289): CRITICAL **: 21:06:08.188: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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      -** (inkscape:5289): CRITICAL **: 21:06:08.188: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
      +** (inkscape:5421): CRITICAL **: 01:31:23.379: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
      +** (inkscape:5421): CRITICAL **: 01:31:23.379: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
      +** (inkscape:5421): CRITICAL **: 01:31:23.379: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
       Failed to get connection
      -** (inkscape:5293): CRITICAL **: 21:06:08.967: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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      -** (inkscape:5293): CRITICAL **: 21:06:08.967: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
      +** (inkscape:5424): CRITICAL **: 01:31:24.128: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
      +** (inkscape:5424): CRITICAL **: 01:31:24.128: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
      +** (inkscape:5424): CRITICAL **: 01:31:24.128: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
       Failed to get connection
      -** (inkscape:5296): CRITICAL **: 21:06:09.824: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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      -** (inkscape:5296): CRITICAL **: 21:06:09.824: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
      +** (inkscape:5427): CRITICAL **: 01:31:24.950: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
      +** (inkscape:5427): CRITICAL **: 01:31:24.950: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
      +** (inkscape:5427): CRITICAL **: 01:31:24.950: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
       
      @@ -104,7 +104,7 @@ plt.show()
  • -

    Total running time of the script: ( 0 minutes 5.655 seconds)

    +

    Total running time of the script: ( 0 minutes 5.141 seconds)

    Dataset Arithmetic (plot_dataset_arithmetic.py)

    00:20.591

    00:18.572

    0.0 MB

    Plot RGB Volume Data (plot_volumeRGB.py)

    00:18.246

    00:17.227

    0.0 MB

    Map from Volume to Vertex Data (plot_volume_to_vertex.py)

    00:08.172

    00:07.047

    0.0 MB

    Plot Volume Data (plot_volume.py)

    00:07.777

    00:06.435

    0.0 MB

    Plot 2D Volume Data (plot_volume2D.py)

    00:07.617

    00:06.264

    0.0 MB

    Plot Vertex Data (plot_vertex.py)

    00:05.277

    00:04.388

    0.0 MB

    Plot RGB Vertex Data (plot_vertexRGB.py)

    00:02.322

    00:01.988

    0.0 MB

    Plot 2D Vertex Data (plot_vertex2D.py)

    00:02.318

    00:01.972

    0.0 MB

    @@ -46,51 +46,51 @@ - + - + - + - + - + - - + + - - + + - + - - + + - - + + - + - + @@ -170,7 +170,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/quickstart/plot_retinotopy_flatmap.html b/auto_examples/quickstart/plot_retinotopy_flatmap.html index 163d4128c..89c37a746 100644 --- a/auto_examples/quickstart/plot_retinotopy_flatmap.html +++ b/auto_examples/quickstart/plot_retinotopy_flatmap.html @@ -6,7 +6,7 @@ - Plot Example Retinotopy Flatmaps — pycortex 1.2.3 documentation + Plot Example Retinotopy Flatmaps — pycortex 1.2.4 documentation @@ -58,13 +58,13 @@

    Out:

    Mask not found, generating...
     Failed to get connection
    -** (inkscape:5302): CRITICAL **: 21:06:15.981: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
    -** (inkscape:5302): CRITICAL **: 21:06:15.981: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
    -** (inkscape:5302): CRITICAL **: 21:06:15.981: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
    +** (inkscape:5434): CRITICAL **: 01:31:30.199: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
    +** (inkscape:5434): CRITICAL **: 01:31:30.199: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
    +** (inkscape:5434): CRITICAL **: 01:31:30.200: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
     Failed to get connection
    -** (inkscape:5305): CRITICAL **: 21:06:17.138: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
    -** (inkscape:5305): CRITICAL **: 21:06:17.138: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
    -** (inkscape:5305): CRITICAL **: 21:06:17.138: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
    +** (inkscape:5438): CRITICAL **: 01:31:31.326: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
    +** (inkscape:5438): CRITICAL **: 01:31:31.326: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
    +** (inkscape:5438): CRITICAL **: 01:31:31.326: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
     
    @@ -100,7 +100,7 @@ plt.show()
    -

    Total running time of the script: ( 0 minutes 7.138 seconds)

    +

    Total running time of the script: ( 0 minutes 6.018 seconds)

    Plot which vertices are inside the same voxels (plot_connected_vertices.py)

    02:02.031

    02:03.094

    0.0 MB

    Plotting a zoomed view of one ROI (plot_zoom_to_roi.py)

    00:40.946

    00:39.235

    0.0 MB

    Animate a series of volumes as a GIF (plot_make_gif.py)

    00:14.490

    00:12.570

    0.0 MB

    Plot a 2D static flatmap (plot_make_figure.py)

    00:12.942

    00:11.182

    0.0 MB

    Plot sulci on the flatmap (plot_sulci.py)

    00:09.918

    00:09.313

    0.0 MB

    Plot ROIs on the flatmap (plot_rois.py)

    00:06.585

    Plot with advanced compositing (plot_advanced_compositing.py)

    00:05.141

    0.0 MB

    Plot with advanced compositing (plot_advanced_compositing.py)

    00:05.655

    Plot ROIs on the flatmap (plot_rois.py)

    00:05.128

    0.0 MB

    Save a 2D static flatmap as PNG (plot_make_png.py)

    00:05.443

    00:04.446

    0.0 MB

    Save a 2D static flatmap as SVG (plot_make_svg.py)

    00:05.388

    Ignore NaN (not-a-number) values in thickness mapping (plot_thickness_nanmean.py)

    00:04.428

    0.0 MB

    Ignore NaN (not-a-number) values in thickness mapping (plot_thickness_nanmean.py)

    00:04.873

    Save a 2D static flatmap as SVG (plot_make_svg.py)

    00:04.189

    0.0 MB

    Plot dropout regions on the flatmap (plot_dropout.py)

    00:03.716

    00:03.200

    0.0 MB

    Plot cutouts on the flatmap (plot_cutouts.py)

    00:02.161

    00:02.057

    0.0 MB

    @@ -46,7 +46,7 @@ - + @@ -134,7 +134,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/quickstart/show_config.html b/auto_examples/quickstart/show_config.html index cb032b49d..1e42755ac 100644 --- a/auto_examples/quickstart/show_config.html +++ b/auto_examples/quickstart/show_config.html @@ -6,7 +6,7 @@ - Finding out where the config and filestore are — pycortex 1.2.3 documentation + Finding out where the config and filestore are — pycortex 1.2.4 documentation @@ -179,7 +179,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/surface_analyses/plot_flatmap_distortion.html b/auto_examples/surface_analyses/plot_flatmap_distortion.html index 6f10a13ab..cfcfe5d24 100644 --- a/auto_examples/surface_analyses/plot_flatmap_distortion.html +++ b/auto_examples/surface_analyses/plot_flatmap_distortion.html @@ -6,7 +6,7 @@ - Flatmap Distortion — pycortex 1.2.3 documentation + Flatmap Distortion — pycortex 1.2.4 documentation @@ -67,11 +67,11 @@ Generating distortion surface info... /home/runner/work/pycortex/pycortex/cortex/polyutils/distortion.py:57: RuntimeWarning: invalid value encountered in true_divide vertratios /= np.bincount(self.polys.ravel(), minlength=len(self.ref)) -/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format +/opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) /home/runner/work/pycortex/pycortex/cortex/polyutils/distortion.py:57: RuntimeWarning: invalid value encountered in true_divide vertratios /= np.bincount(self.polys.ravel(), minlength=len(self.ref)) -/opt/hostedtoolcache/Python/3.9.10/x64/lib/python3.9/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format +/opt/hostedtoolcache/Python/3.9.12/x64/lib/python3.9/site-packages/scipy/sparse/linalg/_dsolve/linsolve.py:322: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) Generating distortion surface info... @@ -125,7 +125,7 @@ plt.show() -

    Total running time of the script: ( 0 minutes 31.399 seconds)

    +

    Total running time of the script: ( 0 minutes 30.161 seconds)

    Plot Example Retinotopy Flatmaps (plot_retinotopy_flatmap.py)

    00:07.138

    00:06.018

    0.0 MB

    Plot Example Retinotopy in Web Viewer (retinotopy_webgl.py)

    @@ -46,27 +46,27 @@ - + - + - + - + - + - + @@ -146,7 +146,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/utils/mni_to_subject.html b/auto_examples/utils/mni_to_subject.html index d8d9061b9..144e32bdf 100644 --- a/auto_examples/utils/mni_to_subject.html +++ b/auto_examples/utils/mni_to_subject.html @@ -6,7 +6,7 @@ - Transform from MNI to Subject Space — pycortex 1.2.3 documentation + Transform from MNI to Subject Space — pycortex 1.2.4 documentation @@ -191,7 +191,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/utils/multi_panels_plots.html b/auto_examples/utils/multi_panels_plots.html index 86eccdca2..846c0dcd3 100644 --- a/auto_examples/utils/multi_panels_plots.html +++ b/auto_examples/utils/multi_panels_plots.html @@ -6,7 +6,7 @@ - Multi-panels figures — pycortex 1.2.3 documentation + Multi-panels figures — pycortex 1.2.4 documentation @@ -222,7 +222,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/utils/plot_get_roi_vertices.html b/auto_examples/utils/plot_get_roi_vertices.html index ef0666214..dcccf93ee 100644 --- a/auto_examples/utils/plot_get_roi_vertices.html +++ b/auto_examples/utils/plot_get_roi_vertices.html @@ -6,7 +6,7 @@ - Get Vertices for an ROI — pycortex 1.2.3 documentation + Get Vertices for an ROI — pycortex 1.2.4 documentation @@ -48,9 +48,9 @@ defined in the SVG ROI file (see /rois.rst).

    plot get roi vertices

    Out:

    Failed to get connection
    -** (inkscape:5395): CRITICAL **: 21:08:33.300: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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    -** (inkscape:5395): CRITICAL **: 21:08:33.300: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
    +** (inkscape:5534): CRITICAL **: 01:33:42.301: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
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     <Figure size 1960x1024 with 2 Axes>
     
    @@ -75,7 +75,7 @@ cortex.quickshow(ffa_map)
    -

    Total running time of the script: ( 0 minutes 2.482 seconds)

    +

    Total running time of the script: ( 0 minutes 2.277 seconds)

    -

    Total running time of the script: ( 0 minutes 0.414 seconds)

    +

    Total running time of the script: ( 0 minutes 0.272 seconds)

    Tissot’s Indicatrix (plot_tissots_indicatrix.py)

    00:34.081

    00:33.731

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    Flatmap Distortion (plot_flatmap_distortion.py)

    00:31.399

    00:30.161

    0.0 MB

    Plot and Use Subsurface Tools (plot_subsurfaces.py)

    00:23.834

    00:22.744

    0.0 MB

    Interpolate Data (plot_interpolate_data.py)

    00:16.019

    00:15.640

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    Plotting Geodesic Distances (plot_geodesic_distance.py)

    00:15.731

    00:14.953

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    Plotting Geodesic Paths (plot_geodesic_path.py)

    00:09.131

    00:08.814

    0.0 MB

    @@ -46,23 +46,23 @@ - + - + - + - + - + @@ -154,7 +154,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/utils/subject_to_mni.html b/auto_examples/utils/subject_to_mni.html index f27f3eeaa..cfb4dfa78 100644 --- a/auto_examples/utils/subject_to_mni.html +++ b/auto_examples/utils/subject_to_mni.html @@ -6,7 +6,7 @@ - Transform from Subject to MNI Space — pycortex 1.2.3 documentation + Transform from Subject to MNI Space — pycortex 1.2.4 documentation @@ -185,7 +185,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/webgl/dynamic_with_custom_template.html b/auto_examples/webgl/dynamic_with_custom_template.html index 6af8e8bc9..32494fa8f 100644 --- a/auto_examples/webgl/dynamic_with_custom_template.html +++ b/auto_examples/webgl/dynamic_with_custom_template.html @@ -6,7 +6,7 @@ - Dynamic viewer with html template — pycortex 1.2.3 documentation + Dynamic viewer with html template — pycortex 1.2.4 documentation @@ -216,7 +216,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/webgl/multiple_datasets.html b/auto_examples/webgl/multiple_datasets.html index bb9672f34..00fac203e 100644 --- a/auto_examples/webgl/multiple_datasets.html +++ b/auto_examples/webgl/multiple_datasets.html @@ -6,7 +6,7 @@ - Create a 3D WebGL Viewer with Multiple Datasets — pycortex 1.2.3 documentation + Create a 3D WebGL Viewer with Multiple Datasets — pycortex 1.2.4 documentation @@ -176,7 +176,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/webgl/single_dataset.html b/auto_examples/webgl/single_dataset.html index 9f2282212..4f4b3ef25 100644 --- a/auto_examples/webgl/single_dataset.html +++ b/auto_examples/webgl/single_dataset.html @@ -6,7 +6,7 @@ - Create a 3D WebGL Viewer — pycortex 1.2.3 documentation + Create a 3D WebGL Viewer — pycortex 1.2.4 documentation @@ -165,7 +165,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/webgl/static.html b/auto_examples/webgl/static.html index 475f65c97..a5b2932c6 100644 --- a/auto_examples/webgl/static.html +++ b/auto_examples/webgl/static.html @@ -6,7 +6,7 @@ - Create a static viewer — pycortex 1.2.3 documentation + Create a static viewer — pycortex 1.2.4 documentation @@ -169,7 +169,7 @@

    Quick search

    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/auto_examples/webgl/static_with_custom_template.html b/auto_examples/webgl/static_with_custom_template.html index 39e3c0148..140e7aebb 100644 --- a/auto_examples/webgl/static_with_custom_template.html +++ b/auto_examples/webgl/static_with_custom_template.html @@ -6,7 +6,7 @@ - Static viewer with html template — pycortex 1.2.3 documentation + Static viewer with html template — pycortex 1.2.4 documentation @@ -221,7 +221,7 @@

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    cortex.align.manual

    -cortex.align.manual(subject, xfmname, reference=None, **kwargs)[source]
    -

    Open GUI for manually aligning a functional volume to the cortical surface for subject. This -creates a new transform called xfm. The name of a nibabel-readable file (e.g. nii) should be +cortex.align.manual(subject, xfmname, output_name='register.lta', wm_color='yellow', pial_color='blue', wm_surface='white', noclean=False, reference=None, inspect_only=False)[source] +

    Open Freesurfer FreeView GUI for manually aligning/adjusting a functional +volume to the cortical surface for subject. This creates a new transform +called xfmname. The name of a nibabel-readable file (e.g. NIfTI) should be supplied as reference. This image will be copied into the database.

    -

    To modify an existing functional-anatomical transform, reference can be left blank, and the -previously used reference will be loaded.

    -

    <<ADD DETAILS ABOUT TRANSFORMATION MATRIX FORMAT HERE>>

    -

    When the GUI is closed, the transform will be saved into the pycortex database. The GUI requires -Mayavi support.

    +

    IMPORTANT: This function assumes that the resulting .lta file is saved as: +“{default folder chosen by FreeView (should be /tmp/fsalign_xxx)}/{output_name}”.

    +

    NOTE: Half-fixed some potential bugs in here, related to assumptions about how +results from mri_info calls would be formatted. IFF .dat files are written +based on nii files that have been stripped of their headers, then there will +be an extra line at the top stating that the coordinates are assumed to be in mm. +Without this line, the code here fails. Seems brittle, ripe for future bugs.

    +

    ALSO: all the freesurfer environment stuff shouldn’t be necessary, except that +I don’t know what vox2ras-tkr is doing.

    +

    Renamed from fs_manual() to manual(), since old manual() function was no longer +supported (or functional) for a while due to changes in mayavi.

    Parameters
    subjectstr

    Subject identifier.

    -
    xfmnamestr

    String identifying the transform to be created or loaded.

    +
    xfmnamestr

    The name of the transform to be modified.

    -
    referencestr, optional

    Path to a nibabel-readable image that will be used as the reference for this transform. -If given the default value of None, this function will attempt to load an existing reference -image from the database.

    +
    output_namestr

    The name of the .lta file generated after FreeView editing.

    -
    kwargsdict

    Passed to mayavi_aligner.get_aligner.

    +
    wm_colorstr | “blue”

    Color of the white matter surface. Default is “blue”. This can +also be adjusted in the FreeView GUI.

    +
    +
    pial_colorstr | “red”

    Color of the pial surface. Default is “red”. This can also be adjusted +the FreeView GUI.

    +
    +
    nocleanboolean | False

    If True, intermediate files will not be removed from /tmp/fsalign_xxx +(this is useful for debugging things), and the returned value will be +the name of the temp directory. Default False.

    +
    +
    referencestr

    name of reference (generally, functional) volume. Only provide this if +you are working from scratch (if no transform exists already), else +it will throw an error.

    +
    +
    inspect_onlyboolean | False

    Whether to open transform to view only (if True, nothing is saved +when freeview is closed)

    +
    +
    wm_surfacestring

    name for white matter surface to use. ‘white’ or ‘smoothwm’

    Returns
    -
    m2D ndarray, shape (4, 4)

    Transformation matrix.

    -
    +
    Nothing unless noclean is true.
    @@ -147,7 +168,7 @@

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    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/generated/cortex.anat.brainmask.html b/generated/cortex.anat.brainmask.html index fc7cad548..b7b3401d1 100644 --- a/generated/cortex.anat.brainmask.html +++ b/generated/cortex.anat.brainmask.html @@ -6,7 +6,7 @@ - cortex.anat.brainmask — pycortex 1.2.3 documentation + cortex.anat.brainmask — pycortex 1.2.4 documentation @@ -117,7 +117,7 @@

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    ©2012, James Gao. | - Powered by Sphinx 4.4.0 + Powered by Sphinx 4.5.0 & Alabaster 0.7.12 | diff --git a/generated/cortex.database.Database.html b/generated/cortex.database.Database.html index fa1c84c95..cc44350df 100644 --- a/generated/cortex.database.Database.html +++ b/generated/cortex.database.Database.html @@ -6,7 +6,7 @@ - cortex.database.Database — pycortex 1.2.3 documentation + cortex.database.Database — pycortex 1.2.4 documentation @@ -49,7 +49,7 @@

    cortex.database.DatabaseMethods

    -

    Get ROI Index Volume (plot_roi_voxel_index_volume.py)

    00:10.143

    00:09.884

    0.0 MB

    Get ROI Voxel Mask (plot_roi_voxel_mask.py)

    00:07.768

    00:07.399

    0.0 MB

    Voxel distance from surface (plot_voxel_distance_from_surface.py)

    00:04.422

    00:04.326

    0.0 MB

    Get Vertices for an ROI (plot_get_roi_vertices.py)

    00:02.482

    00:02.277

    0.0 MB

    Mosaic plot (plot_mosaic.py)

    00:00.414

    00:00.272

    0.0 MB

    Transform from MNI to Subject Space (mni_to_subject.py)

    +
    @@ -118,7 +118,7 @@

    cortex.database.DatabaseAttributes

    -

    +
    @@ -206,7 +206,7 @@

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    ©2012, James Gao. | - Powered by
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    cortex.dataset.Datasetcortex.webshow, it will automatically be converted into a Dataset.

    All kwargs should be BrainData or Dataset objects.

    Methods

    -

    +
    @@ -160,7 +160,7 @@

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    cortex.dataset.Vertex

    Methods

    -

    +
    @@ -111,7 +111,7 @@

    cortex.dataset.Vertex

    Attributes

    - +
    @@ -217,7 +217,7 @@

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    cortex.dataset.Vertex2D

    Methods

    -

    +
    @@ -100,7 +100,7 @@

    cortex.dataset.Vertex2D

    Attributes

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    @@ -197,7 +197,7 @@

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    cortex.dataset.VertexRGBMethods

    -

    +
    @@ -103,7 +103,7 @@

    cortex.dataset.VertexRGBAttributes

    -

    +
    @@ -206,7 +206,7 @@

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    cortex.dataset.Volume

    Methods

    -

    +
    @@ -118,7 +118,7 @@

    cortex.dataset.Volume

    Attributes

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    @@ -218,7 +218,7 @@

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    cortex.dataset.Volume2D

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    @@ -100,7 +100,7 @@

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    @@ -197,7 +197,7 @@

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    cortex.dataset.VolumeRGBMethods

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    +
    @@ -130,7 +130,7 @@

    cortex.dataset.VolumeRGBAttributes

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    @@ -227,7 +227,7 @@

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\ No newline at end of file diff --git a/segmentation.html b/segmentation.html index 5576c9cdc..c56df324f 100644 --- a/segmentation.html +++ b/segmentation.html @@ -6,7 +6,7 @@ - Segmentation Tutorial — pycortex 1.2.3 documentation + Segmentation Tutorial — pycortex 1.2.4 documentation @@ -132,7 +132,7 @@

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