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Fix issue #283: Rename Key Group to Entity Set #329

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merged 7 commits into from
Oct 10, 2024
Merged

Fix issue #283: Rename Key Group to Entity Set #329

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c230792
Fix issue #283: Rename Key Group to Entity Set
tientong98 Oct 4, 2024
68b4962
Fix linting issues
tientong98 Oct 4, 2024
a3ce6fc
Update to ubuntu 2404:2024.08.1 and [email protected]
tientong98 Oct 9, 2024
701e667
debug circleci after updating bids-validator to 1.14.14-dev.0
tientong98 Oct 9, 2024
c1b6995
fix build_validator_call in cubids/validator.py
tientong98 Oct 9, 2024
bee52cd
Revert changes in HISTORY.rst so that changelog is not modified
tientong98 Oct 9, 2024
87fcefc
Update docs/usage.rst
tientong98 Oct 9, 2024
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6 changes: 3 additions & 3 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ jobs:
type: string
default: "3.8"
machine:
image: ubuntu-2004:202201-02
image: ubuntu-2404:2024.08.1
working_directory: /home/circleci/src/CuBIDS
steps:
- checkout:
Expand All @@ -34,7 +34,7 @@ jobs:
# Add nodejs and the validator
conda install nodejs
npm install -g yarn && \
npm install -g bids-validator
npm install -g bids-validator@1.14.14-dev.0

# Install CuBIDS
pip install -e .[tests]
Expand Down Expand Up @@ -83,7 +83,7 @@ jobs:

deploy_pypi:
machine:
image: ubuntu-2004:202201-02
image: ubuntu-2404:2024.08.1
working_directory: /home/circleci/src/CuBIDS
steps:
- checkout:
Expand Down
4 changes: 2 additions & 2 deletions cubids/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,7 +230,7 @@ def _parse_apply():
action="store",
help=(
"path to the _summary.tsv that has been edited "
"in the MergeInto and RenameKeyGroup columns. If the "
"in the MergeInto and RenameEntitySet columns. If the "
" summary table is located in the code/CuBIDS "
"directory, then users can just pass the summary tsv "
"filename instead of the full path to the tsv"
Expand All @@ -242,7 +242,7 @@ def _parse_apply():
action="store",
help=(
"path to the _files.tsv that has been edited "
"in the MergeInto and RenameKeyGroup columns. If the "
"in the MergeInto and RenameEntitySet columns. If the "
"files table is located in the code/CuBIDS "
"directory, then users can just pass the files tsv "
"filename instead of the full path to the tsv"
Expand Down
4 changes: 2 additions & 2 deletions cubids/constants.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
"""Constants for CuBIDS."""

# Names of identifier variables.
# Used to place KeyGroup and ParamGroup at the beginning of a dataframe,
# Used to place EntitySet and ParamGroup at the beginning of a dataframe,
# but both are hardcoded in the relevant function.
ID_VARS = set(["KeyGroup", "ParamGroup", "FilePath"])
ID_VARS = set(["EntitySet", "ParamGroup", "FilePath"])
# Entities that should not be used to group parameter sets
NON_KEY_ENTITIES = set(["subject", "session", "extension"])
# Multi-dimensional keys SliceTiming XXX: what is this line about?
Expand Down
172 changes: 87 additions & 85 deletions cubids/cubids.py
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Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions cubids/data/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -177,13 +177,13 @@ relational_params:
FieldmapKey:
# can be
# "bool": a single column with true if an IntendedFor is present
# "columns": List all intended key groups in separate columns (IntendedForXX)
# "columns": List all intended entity sets in separate columns (IntendedForXX)
display_mode: bool
suggest_variant_rename: yes
IntendedForKey:
# can be
# "bool": a single column with true if an IntendedFor is present
# "columns": List all intended key groups in separate columns (IntendedForXX)
# "columns": List all intended entity sets in separate columns (IntendedForXX)
display_mode: bool
suggest_variant_rename: yes
# BIDS fields to directly include in the Parameter Groupings
Expand Down
12 changes: 7 additions & 5 deletions cubids/metadata_merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,10 +54,10 @@ def _check_sdc_cols(meta1, meta2):

needs_merge = actions[np.isfinite(actions["MergeInto"])]
for _, row_needs_merge in needs_merge.iterrows():
source_param_key = tuple(row_needs_merge[["MergeInto", "KeyGroup"]])
dest_param_key = tuple(row_needs_merge[["ParamGroup", "KeyGroup"]])
source_param_key = tuple(row_needs_merge[["MergeInto", "EntitySet"]])
dest_param_key = tuple(row_needs_merge[["ParamGroup", "EntitySet"]])
dest_metadata = row_needs_merge.to_dict()
source_row = actions.loc[(actions[["ParamGroup", "KeyGroup"]] == source_param_key).all(1)]
source_row = actions.loc[(actions[["ParamGroup", "EntitySet"]] == source_param_key).all(1)]

if source_param_key[0] == 0:
print("going to delete ", dest_param_key)
Expand Down Expand Up @@ -299,10 +299,12 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):

if acq_group_level == "subject":
acq_id = (file_entities.get("subject"), file_entities.get("session"))
acq_groups[acq_id].append((row.KeyGroup, row.ParamGroup))
acq_groups[acq_id].append((row.EntitySet, row.ParamGroup))
else:
acq_id = (file_entities.get("subject"), None)
acq_groups[acq_id].append((row.KeyGroup, row.ParamGroup, file_entities.get("session")))
acq_groups[acq_id].append(
(row.EntitySet, row.ParamGroup, file_entities.get("session"))
)

# Map the contents to a list of subjects/sessions
contents_to_subjects = defaultdict(list)
Expand Down
2 changes: 1 addition & 1 deletion cubids/tests/data/BIDS_Dataset/README
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Heavily downsampled CS-DSI testing datasets

This data has had some parameters changed so that there are different
parameter groups in the same key groups.
parameter groups in the same entity sets.

## Changes

Expand Down
40 changes: 20 additions & 20 deletions cubids/tests/data/CuBIDS_Toy_Dataset_Curation/v0_files.csv
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
KeyParamGroup,KeyGroup,ParamGroup,Counts,Dim1Size,Dim2Size,Dim3Size,EchoTime,EffectiveEchoSpacing,FlipAngle,HasFieldmap,KeyGroupCount,Modality,NSliceTimes,NumVolumes,Obliquity,PartialFourier,PhaseEncodingDirection,RepetitionTime,TotalReadoutTime,UsedAsFieldmap,VoxelSizeDim1,VoxelSizeDim2,VoxelSizeDim3,FilePath
datatype-anat_suffix-T1w__1,datatype-anat_suffix-T1w,1,3,180,216,180,0.0029,,8.0,FALSE,3,anat,0,1.0,FALSE,,i-,2.5,,FALSE,1.0,1.0,1.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz
datatype-anat_suffix-T1w__1,datatype-anat_suffix-T1w,1,3,180,216,180,0.0029,,8.0,FALSE,3,anat,0,1.0,FALSE,,i-,2.5,,FALSE,1.0,1.0,1.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.nii.gz
datatype-anat_suffix-T1w__1,datatype-anat_suffix-T1w,1,3,180,216,180,0.0029,,8.0,FALSE,3,anat,0,1.0,FALSE,,i-,2.5,,FALSE,1.0,1.0,1.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/anat/sub-03_ses-phdiff_T1w.nii.gz
acquisition-HASC55AP_datatype-dwi_suffix-dwi__1,acquisition-HASC55AP_datatype-dwi_suffix-dwi,1,1,36,43,36,0.04,0.00069,90.0,TRUE,3,dwi,36,61.0,FALSE,,j,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz
acquisition-HASC55AP_datatype-dwi_suffix-dwi__2,acquisition-HASC55AP_datatype-dwi_suffix-dwi,2,1,36,43,36,0.089,0.00069,,TRUE,3,dwi,36,61.0,FALSE,,j,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.nii.gz
acquisition-HASC55AP_datatype-dwi_suffix-dwi__3,acquisition-HASC55AP_datatype-dwi_suffix-dwi,3,1,36,43,36,0.089,0.00069,90.0,TRUE,3,dwi,36,61.0,FALSE,,j,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.nii.gz
acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1__1,acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1,1,3,36,43,36,0.004,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz
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acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1__1,acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1,1,3,36,43,36,0.004,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude1.nii.gz
acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2__1,acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2,1,3,36,43,36,0.006,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz
acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2__1,acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2,1,3,36,43,36,0.006,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude2.nii.gz
acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2__1,acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2,1,3,36,43,36,0.006,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude2.nii.gz
acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff__1,acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff,1,3,36,43,36,,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz
acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff__1,acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff,1,3,36,43,36,,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_phasediff.nii.gz
acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff__1,acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff,1,3,36,43,36,,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz
datatype-fmap_direction-PA_fmap-epi_suffix-epi__1,datatype-fmap_direction-PA_fmap-epi_suffix-epi,1,2,36,43,36,0.089,0.00069,90.0,FALSE,3,fmap,36,1.0,FALSE,,j-,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz
datatype-fmap_direction-PA_fmap-epi_suffix-epi__1,datatype-fmap_direction-PA_fmap-epi_suffix-epi,1,2,36,43,36,0.089,0.00069,90.0,FALSE,3,fmap,36,1.0,FALSE,,j-,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_dir-PA_epi.nii.gz
datatype-fmap_direction-PA_fmap-epi_suffix-epi__2,datatype-fmap_direction-PA_fmap-epi_suffix-epi,2,1,36,43,36,0.089,0.00069,90.0,FALSE,3,fmap,36,1.0,FALSE,,j-,4.2,0.072,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.nii.gz
datatype-func_suffix-bold_task-rest__1,datatype-func_suffix-bold_task-rest,1,1,36,43,36,0.089,0.00069,90.0,FALSE,2,func,36,61.0,FALSE,,j,1.0,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/func/sub-03_ses-phdiff_task-rest_bold.nii.gz
KeyParamGroup,EntitySet,ParamGroup,Counts,Dim1Size,Dim2Size,Dim3Size,EchoTime,EffectiveEchoSpacing,FlipAngle,HasFieldmap,EntitySetCount,Modality,NSliceTimes,NumVolumes,Obliquity,PartialFourier,PhaseEncodingDirection,RepetitionTime,TotalReadoutTime,UsedAsFieldmap,VoxelSizeDim1,VoxelSizeDim2,VoxelSizeDim3,FilePath
datatype-anat_suffix-T1w__1,datatype-anat_suffix-T1w,1,3,180,216,180,0.0029,,8.0,FALSE,3,anat,0,1.0,FALSE,,i-,2.5,,FALSE,1.0,1.0,1.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz
datatype-anat_suffix-T1w__1,datatype-anat_suffix-T1w,1,3,180,216,180,0.0029,,8.0,FALSE,3,anat,0,1.0,FALSE,,i-,2.5,,FALSE,1.0,1.0,1.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.nii.gz
datatype-anat_suffix-T1w__1,datatype-anat_suffix-T1w,1,3,180,216,180,0.0029,,8.0,FALSE,3,anat,0,1.0,FALSE,,i-,2.5,,FALSE,1.0,1.0,1.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/anat/sub-03_ses-phdiff_T1w.nii.gz
acquisition-HASC55AP_datatype-dwi_suffix-dwi__1,acquisition-HASC55AP_datatype-dwi_suffix-dwi,1,1,36,43,36,0.04,0.00069,90.0,TRUE,3,dwi,36,61.0,FALSE,,j,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz
acquisition-HASC55AP_datatype-dwi_suffix-dwi__2,acquisition-HASC55AP_datatype-dwi_suffix-dwi,2,1,36,43,36,0.089,0.00069,,TRUE,3,dwi,36,61.0,FALSE,,j,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.nii.gz
acquisition-HASC55AP_datatype-dwi_suffix-dwi__3,acquisition-HASC55AP_datatype-dwi_suffix-dwi,3,1,36,43,36,0.089,0.00069,90.0,TRUE,3,dwi,36,61.0,FALSE,,j,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.nii.gz
acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1__1,acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1,1,3,36,43,36,0.004,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz
acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1__1,acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1,1,3,36,43,36,0.004,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude1.nii.gz
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acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff__1,acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff,1,3,36,43,36,,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_phasediff.nii.gz
acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff__1,acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff,1,3,36,43,36,,,60.0,FALSE,3,fmap,0,1.0,FALSE,0.75,j-,1.5,,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz
datatype-fmap_direction-PA_fmap-epi_suffix-epi__1,datatype-fmap_direction-PA_fmap-epi_suffix-epi,1,2,36,43,36,0.089,0.00069,90.0,FALSE,3,fmap,36,1.0,FALSE,,j-,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz
datatype-fmap_direction-PA_fmap-epi_suffix-epi__1,datatype-fmap_direction-PA_fmap-epi_suffix-epi,1,2,36,43,36,0.089,0.00069,90.0,FALSE,3,fmap,36,1.0,FALSE,,j-,4.2,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_dir-PA_epi.nii.gz
datatype-fmap_direction-PA_fmap-epi_suffix-epi__2,datatype-fmap_direction-PA_fmap-epi_suffix-epi,2,1,36,43,36,0.089,0.00069,90.0,FALSE,3,fmap,36,1.0,FALSE,,j-,4.2,0.072,TRUE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.nii.gz
datatype-func_suffix-bold_task-rest__1,datatype-func_suffix-bold_task-rest,1,1,36,43,36,0.089,0.00069,90.0,FALSE,2,func,36,61.0,FALSE,,j,1.0,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-03/ses-phdiff/func/sub-03_ses-phdiff_task-rest_bold.nii.gz
datatype-func_suffix-bold_task-rest__2,datatype-func_suffix-bold_task-rest,2,1,36,43,36,0.089,0.00069,90.0,TRUE,2,func,36,10.0,FALSE,,j,1.0,0.072,FALSE,5.0,5.0,5.0,/Users/scovitz/BIDS_Dataset_Datalad/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.nii.gz
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