Renamed modules to make them more consistent with commands

_other/drafts/ANOVA_draft.py

@@ -10,7 +10,7 @@
 from statsmodels.stats.anova import anova_lm
 
 from unravel.cluster_stats.stats import cluster_validation_data_df
-from unravel.cluster_stats.stats_table import valid_clusters_summary
+from unravel.cluster_stats.stats_table import cluster_summary
 from unravel.core.argparse_utils import SuppressMetavar, SM
 
 
@@ -203,7 +203,7 @@ def main():
         raw_data_df.to_csv(validation_info_csv, index=False)
 
     # Concat all cluster_validation_info.csv files
-    valid_clusters_summary(f'cluster_validation_info_ANOVA_{args.valid_criterion}.csv', f'cluster_validation_summary_ANOVA_{args.valid_criterion}.csv')
+    cluster_summary(f'cluster_validation_info_ANOVA_{args.valid_criterion}.csv', f'cluster_validation_summary_ANOVA_{args.valid_criterion}.csv')
 
 
 if __name__ == '__main__':

pyproject.toml

@@ -66,7 +66,7 @@ requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project.scripts]
-unravel_commands = "unravel.command_list:main"
+unravel_commands = "unravel.unravel_commands:main"
 atlas_relabel = "unravel.image_tools.atlas.relable_nii:main"
 atlas_wireframe = "unravel.image_tools.atlas.wireframe:main"
 cluster_fdr_range = "unravel.cluster_stats.fdr_range:main"
@@ -81,45 +81,45 @@ cluster_legend = "unravel.cluster_stats.legend:main"
 cluster_org_data = "unravel.cluster_stats.org_data:main"
 cluster_prism = "unravel.cluster_stats.prism:main"
 cluster_stats = "unravel.cluster_stats.stats:main"
-cluster_summary = "unravel.cluster_stats.valid_clusters_summary:main"
+cluster_summary = "unravel.cluster_stats.cluster_summary:main"
 cluster_table = "unravel.cluster_stats.table:main"
-cluster_validation = "unravel.cluster_stats.validate_clusters:main"
-cluster_crop = "unravel.cluster_stats.crop_clusters:main"
+cluster_validation = "unravel.cluster_stats.cluster_validation:main"
+cluster_crop = "unravel.cluster_stats.crop:main"
 effect_sizes = "unravel.cluster_stats.effect_sizes.effect_sizes:main"
 effect_sizes_sex_abs = "unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute:main"
 effect_sizes_sex_rel = "unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative:main"
 io_h5_to_tifs = "unravel.image_io.h5_to_tifs:main"
-io_img = "unravel.image_io.img_io:main"
+io_img = "unravel.image_io.io_img:main"
 io_img_to_npy = "unravel.image_io.img_to_npy:main"
 io_metadata = "unravel.image_io.metadata:main"
 io_nii_hd = "unravel.image_io.nii_hd:main"
 io_nii_info = "unravel.image_io.nii_info:main"
-io_nii = "unravel.image_io.nii_io:main"
+io_nii = "unravel.image_io.io_nii:main"
 io_nii_to_tifs = "unravel.image_io.nii_to_tifs:main"
 io_nii_to_zarr = "unravel.image_io.nii_to_zarr:main"
 io_reorient_nii = "unravel.image_io.reorient_nii:main"
 io_tif_to_tifs = "unravel.image_io.tif_to_tifs:main"
 io_zarr_to_nii = "unravel.image_io.zarr_to_nii:main"
 img_avg = "unravel.image_tools.avg:main"
 img_bbox = "unravel.image_tools.bbox:main"
-img_extend = "unravel.image_tools.extend_image:main"
+img_extend = "unravel.image_tools.extend:main"
 img_max = "unravel.image_tools.max:main"
-img_pad = "unravel.image_tools.pad_img:main"
+img_pad = "unravel.image_tools.pad:main"
 img_spatial_avg = "unravel.image_tools.spatial_averaging:main"
-img_DoG = "unravel.image_tools.tif_DoG:main"
-img_rb = "unravel.image_tools.tif_rb:main"
+img_DoG = "unravel.image_tools.DoG:main"
+img_rb = "unravel.image_tools.rb:main"
 img_transpose = "unravel.image_tools.transpose_axes:main"
-img_unique = "unravel.image_tools.uniq_intensities:main"
+img_unique = "unravel.image_tools.unique_intensities:main"
 rstats_summary = "unravel.region_stats.rstats_summary:main"
 rstats = "unravel.region_stats.rstats:main"
 rstats_mean_IF = "unravel.region_stats.rstats_mean_IF:main"
 rstats_mean_IF_in_seg = "unravel.region_stats.rstats_mean_IF_in_segmented_voxels:main"
 rstats_mean_IF_summary = "unravel.region_stats.rstats_mean_IF_summary:main"
 reg_affine_initializer = "unravel.register.affine_initializer:main"
-reg_check_mask = "unravel.register.check_brain_mask:main"
-reg_check = "unravel.register.check_reg:main"
-reg_prep = "unravel.register.prep_reg:main"
+reg_check_brain_mask = "unravel.register.reg_check_brain_mask:main"
+reg_prep = "unravel.register.reg_prep:main"
 reg = "unravel.register.reg:main"
+reg_check = "unravel.register.reg_check:main"
 seg_brain_mask = "unravel.segment.brain_mask:main"
 seg_copy_tifs = "unravel.segment.copy_tifs:main"
 seg_ilastik = "unravel.segment.ilastik_pixel_classification:main"
@@ -133,7 +133,7 @@ vstats_apply_mask = "unravel.voxel_stats.apply_mask:main"
 vstats_hemi_to_avg = "unravel.voxel_stats.hemi_to_LR_avg:main"
 vstats_whole_to_avg = "unravel.voxel_stats.whole_to_LR_avg:main"
 vstats_mirror = "unravel.voxel_stats.mirror:main"
-vstats_prep = "unravel.voxel_stats.prep_vstats:main"
+vstats_prep = "unravel.voxel_stats.vstats_prep:main"
 vstats = "unravel.voxel_stats.vstats:main"
 vstats_z_score = "unravel.voxel_stats.z_score:main"
 warp_to_atlas = "unravel.warp.to_atlas:main"

unravel/cluster_stats/__init__.py

@@ -1,5 +0,0 @@
-# unravel/cluster_stats/__init__.py
-
-# from unravel.cluster_stats.effect_sizes import effect_sizes
-# from unravel.cluster_stats.stats_table import valid_clusters_summary
-# from .stats import cluster_validation_data_df

unravel/cluster_stats/valid_clusters_summary.py → unravel/cluster_stats/cluster_summary.py

@@ -46,7 +46,7 @@
 
 def parse_args():
     parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
-    parser.add_argument('-c', '--config', help='Path to the config.ini file. Default: unravel/cluster_stats/valid_clusters_summary.ini', default=Path(__file__).parent / 'valid_clusters_summary.ini', action=SM)
+    parser.add_argument('-c', '--config', help='Path to the config.ini file. Default: unravel/cluster_stats/cluster_summary.ini', default=Path(__file__).parent / 'cluster_summary.ini', action=SM)
 
     # cluster_org_data -e <list of experiment directories> -cvd '*' -td <target_dir> -vd <path/vstats_dir> -v
     parser.add_argument('-e', '--exp_paths', help='List of experiment dir paths w/ sample?? dirs to process. (needed for cluster_org_data)', nargs='*', action=SM)

unravel/cluster_stats/stats.py

@@ -58,7 +58,7 @@
 from unravel.core.argparse_utils import SuppressMetavar, SM
 from unravel.core.config import Configuration
 from unravel.core.utils import initialize_progress_bar, print_cmd_and_times
-from unravel.cluster_stats.stats_table import valid_clusters_summary
+from unravel.cluster_stats.stats_table import cluster_summary
 
 def parse_args():
     parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
@@ -402,9 +402,9 @@ def main():
 
     # Concat all cluster_validation_info.csv files
     if len(args.groups) == 2:
-        valid_clusters_summary('cluster_validation_info_t-test.csv', 'cluster_validation_summary_t-test.csv')
+        cluster_summary('cluster_validation_info_t-test.csv', 'cluster_validation_summary_t-test.csv')
     else:
-        valid_clusters_summary('cluster_validation_info_tukey.csv', 'cluster_validation_summary_tukey.csv')
+        cluster_summary('cluster_validation_info_tukey.csv', 'cluster_validation_summary_tukey.csv')
 
 
 if __name__ == '__main__':

unravel/cluster_stats/stats_table.py

@@ -24,7 +24,7 @@ def parse_args():
     parser.epilog = __doc__
     return parser.parse_args()
 
-def valid_clusters_summary(csv_pattern, output):
+def cluster_summary(csv_pattern, output):
     # Use glob to find all matching CSV files recursively
     csv_files = glob(str(f'**/{csv_pattern}'), recursive=True)
     if not csv_files:
@@ -46,7 +46,7 @@ def valid_clusters_summary(csv_pattern, output):
 def main():
     args = parse_args()
 
-    valid_clusters_summary(args.csv_pattern, args.output)
+    cluster_summary(args.csv_pattern, args.output)
 
 
 if __name__ == '__main__':

unravel/core/img_tools.py

@@ -5,7 +5,7 @@
     - resample: Resample a 3D ndarray.
     - reorient_for_raw_to_nii_conv: Reorient an ndarray for registration or warping to atlas space
     - pixel_classification: Segment tif series with Ilastik.
-    - pad_img: Pad an ndarray by a specified percentage.
+    - pad: Pad an ndarray by a specified percentage.
     - reorient_ndarray: Reorient a 3D ndarray based on the 3 letter orientation code (using the letters RLAPSI).
     - reorient_ndarray2: Reorient a 3D ndarray based on the 3 letter orientation code (using the letters RLAPSI).
     - rolling_ball_subtraction_opencv_parallel: Subtract background from a 3D ndarray using OpenCV.
@@ -102,7 +102,7 @@ def pixel_classification(tif_dir, ilastik_project, output_dir, ilastik_log=None)
         print("\n    Ilastik completed successfully.\n")
 
 @print_func_name_args_times()
-def pad_img(ndarray, pad_width=0.15):
+def pad(ndarray, pad_width=0.15):
     """Pads ndarray by 15% of voxels on all sides"""
     pad_factor = 1 + 2 * pad_width
     pad_width_x = round(((ndarray.shape[0] * pad_factor) - ndarray.shape[0]) / 2)

unravel/docs/_build/html/_modules/index.html

@@ -347,7 +347,9 @@
 
   <h1>All modules for which code is available</h1>
 <ul><li><a href="unravel/cluster_stats/brain_model.html">unravel.cluster_stats.brain_model</a></li>
-<li><a href="unravel/cluster_stats/crop_clusters.html">unravel.cluster_stats.crop_clusters</a></li>
+<li><a href="unravel/cluster_stats/cluster_summary.html">unravel.cluster_stats.cluster_summary</a></li>
+<li><a href="unravel/cluster_stats/cluster_validation.html">unravel.cluster_stats.cluster_validation</a></li>
+<li><a href="unravel/cluster_stats/crop.html">unravel.cluster_stats.crop</a></li>
 <li><a href="unravel/cluster_stats/effect_sizes/effect_sizes.html">unravel.cluster_stats.effect_sizes.effect_sizes</a></li>
 <li><a href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html">unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute</a></li>
 <li><a href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html">unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative</a></li>
@@ -364,52 +366,50 @@ <h1>All modules for which code is available</h1>
 <li><a href="unravel/cluster_stats/stats_table.html">unravel.cluster_stats.stats_table</a></li>
 <li><a href="unravel/cluster_stats/sunburst.html">unravel.cluster_stats.sunburst</a></li>
 <li><a href="unravel/cluster_stats/table.html">unravel.cluster_stats.table</a></li>
-<li><a href="unravel/cluster_stats/valid_clusters_summary.html">unravel.cluster_stats.valid_clusters_summary</a></li>
-<li><a href="unravel/cluster_stats/validate_clusters.html">unravel.cluster_stats.validate_clusters</a></li>
-<li><a href="unravel/command_list.html">unravel.command_list</a></li>
 <li><a href="unravel/core/argparse_utils.html">unravel.core.argparse_utils</a></li>
 <li><a href="unravel/core/argparse_utils_rich.html">unravel.core.argparse_utils_rich</a></li>
 <li><a href="unravel/core/config.html">unravel.core.config</a></li>
 <li><a href="unravel/core/img_io.html">unravel.core.img_io</a></li>
 <li><a href="unravel/core/img_tools.html">unravel.core.img_tools</a></li>
 <li><a href="unravel/core/utils.html">unravel.core.utils</a></li>
 <li><a href="unravel/image_io/h5_to_tifs.html">unravel.image_io.h5_to_tifs</a></li>
-<li><a href="unravel/image_io/img_io.html">unravel.image_io.img_io</a></li>
 <li><a href="unravel/image_io/img_to_npy.html">unravel.image_io.img_to_npy</a></li>
+<li><a href="unravel/image_io/io_img.html">unravel.image_io.io_img</a></li>
+<li><a href="unravel/image_io/io_nii.html">unravel.image_io.io_nii</a></li>
 <li><a href="unravel/image_io/metadata.html">unravel.image_io.metadata</a></li>
 <li><a href="unravel/image_io/nii_hd.html">unravel.image_io.nii_hd</a></li>
 <li><a href="unravel/image_io/nii_info.html">unravel.image_io.nii_info</a></li>
-<li><a href="unravel/image_io/nii_io.html">unravel.image_io.nii_io</a></li>
 <li><a href="unravel/image_io/nii_to_tifs.html">unravel.image_io.nii_to_tifs</a></li>
 <li><a href="unravel/image_io/nii_to_zarr.html">unravel.image_io.nii_to_zarr</a></li>
 <li><a href="unravel/image_io/reorient_nii.html">unravel.image_io.reorient_nii</a></li>
 <li><a href="unravel/image_io/tif_to_tifs.html">unravel.image_io.tif_to_tifs</a></li>
 <li><a href="unravel/image_io/zarr_to_nii.html">unravel.image_io.zarr_to_nii</a></li>
+<li><a href="unravel/image_tools/DoG.html">unravel.image_tools.DoG</a></li>
 <li><a href="unravel/image_tools/atlas/relabel_nii.html">unravel.image_tools.atlas.relabel_nii</a></li>
 <li><a href="unravel/image_tools/atlas/wireframe.html">unravel.image_tools.atlas.wireframe</a></li>
 <li><a href="unravel/image_tools/avg.html">unravel.image_tools.avg</a></li>
 <li><a href="unravel/image_tools/bbox.html">unravel.image_tools.bbox</a></li>
-<li><a href="unravel/image_tools/extend_image.html">unravel.image_tools.extend_image</a></li>
+<li><a href="unravel/image_tools/extend.html">unravel.image_tools.extend</a></li>
 <li><a href="unravel/image_tools/max.html">unravel.image_tools.max</a></li>
-<li><a href="unravel/image_tools/pad_img.html">unravel.image_tools.pad_img</a></li>
+<li><a href="unravel/image_tools/pad.html">unravel.image_tools.pad</a></li>
+<li><a href="unravel/image_tools/rb.html">unravel.image_tools.rb</a></li>
 <li><a href="unravel/image_tools/spatial_averaging.html">unravel.image_tools.spatial_averaging</a></li>
-<li><a href="unravel/image_tools/tif_DoG.html">unravel.image_tools.tif_DoG</a></li>
-<li><a href="unravel/image_tools/tif_rb.html">unravel.image_tools.tif_rb</a></li>
 <li><a href="unravel/image_tools/transpose_axes.html">unravel.image_tools.transpose_axes</a></li>
-<li><a href="unravel/image_tools/uniq_intensities.html">unravel.image_tools.uniq_intensities</a></li>
+<li><a href="unravel/image_tools/unique_intensities.html">unravel.image_tools.unique_intensities</a></li>
 <li><a href="unravel/region_stats/rstats.html">unravel.region_stats.rstats</a></li>
 <li><a href="unravel/region_stats/rstats_mean_IF.html">unravel.region_stats.rstats_mean_IF</a></li>
 <li><a href="unravel/region_stats/rstats_mean_IF_in_segmented_voxels.html">unravel.region_stats.rstats_mean_IF_in_segmented_voxels</a></li>
 <li><a href="unravel/region_stats/rstats_mean_IF_summary.html">unravel.region_stats.rstats_mean_IF_summary</a></li>
 <li><a href="unravel/region_stats/rstats_summary.html">unravel.region_stats.rstats_summary</a></li>
 <li><a href="unravel/register/affine_initializer.html">unravel.register.affine_initializer</a></li>
-<li><a href="unravel/register/check_brain_mask.html">unravel.register.check_brain_mask</a></li>
-<li><a href="unravel/register/check_reg.html">unravel.register.check_reg</a></li>
-<li><a href="unravel/register/prep_reg.html">unravel.register.prep_reg</a></li>
 <li><a href="unravel/register/reg.html">unravel.register.reg</a></li>
+<li><a href="unravel/register/reg_check.html">unravel.register.reg_check</a></li>
+<li><a href="unravel/register/reg_check_brain_mask.html">unravel.register.reg_check_brain_mask</a></li>
+<li><a href="unravel/register/reg_prep.html">unravel.register.reg_prep</a></li>
 <li><a href="unravel/segment/brain_mask.html">unravel.segment.brain_mask</a></li>
 <li><a href="unravel/segment/copy_tifs.html">unravel.segment.copy_tifs</a></li>
 <li><a href="unravel/segment/ilastik_pixel_classification.html">unravel.segment.ilastik_pixel_classification</a></li>
+<li><a href="unravel/unravel_commands.html">unravel.unravel_commands</a></li>
 <li><a href="unravel/utilities/aggregate_files_from_sample_dirs.html">unravel.utilities.aggregate_files_from_sample_dirs</a></li>
 <li><a href="unravel/utilities/aggregate_files_w_recursive_search.html">unravel.utilities.aggregate_files_w_recursive_search</a></li>
 <li><a href="unravel/utilities/clean_tif_dirs.html">unravel.utilities.clean_tif_dirs</a></li>
@@ -421,8 +421,8 @@ <h1>All modules for which code is available</h1>
 <li><a href="unravel/voxel_stats/mirror.html">unravel.voxel_stats.mirror</a></li>
 <li><a href="unravel/voxel_stats/other/IF_outliers.html">unravel.voxel_stats.other.IF_outliers</a></li>
 <li><a href="unravel/voxel_stats/other/r_to_p.html">unravel.voxel_stats.other.r_to_p</a></li>
-<li><a href="unravel/voxel_stats/prep_vstats.html">unravel.voxel_stats.prep_vstats</a></li>
 <li><a href="unravel/voxel_stats/vstats.html">unravel.voxel_stats.vstats</a></li>
+<li><a href="unravel/voxel_stats/vstats_prep.html">unravel.voxel_stats.vstats_prep</a></li>
 <li><a href="unravel/voxel_stats/whole_to_LR_avg.html">unravel.voxel_stats.whole_to_LR_avg</a></li>
 <li><a href="unravel/voxel_stats/z_score.html">unravel.voxel_stats.z_score</a></li>
 <li><a href="unravel/warp/to_atlas.html">unravel.warp.to_atlas</a></li>