Add data with multiple parameter groups.

bond/bond.py

@@ -1,6 +1,10 @@
 """Main module."""
 from pathlib import Path
+import bids
+bids.config.set_option('extension_initial_dot', True)
+from bids.util import parse_file_entities
 
+NON_KEY_ENTITIES = set(["subject", "session", "extension"])
 
 class BOnD(object):
 
@@ -11,12 +15,14 @@ def fieldmaps_ok(self):
  pass
 
  def rename_files(self, pattern, replacement):
+ """
  # @Params
  # - path: a string contianing the path to the bids directory inside which we want to change files
  # - pattern: the substring of the file we would like to replace
  # - replacement: the substring that will replace "pattern"
  # @Returns
  # - None
+ """
  files_and_dirs = Path(self.path).rglob('*')
  for path in files_and_dirs:
  old_name = path.stem
@@ -25,9 +31,55 @@ def rename_files(self, pattern, replacement):
  new_name = old_name.replace(pattern, replacement) + old_ext
  path.rename(Path(directory, new_name))
 
- def find_param_sets(self, pattern):
- pass
+ def get_param_groups(self, key_group):
+ key_entities = _key_group_to_entities(key_group)
+ matching_files = self.layout.get(return_type="file", scope="self",
+ **key_entities)
+ return _get_param_groups(matching_files)
+
+ def get_key_groups(self):
+ key_groups = set()
+ for path in Path(self.path).rglob("*.*"):
+ if path.suffix == ".json":
+ continue
+ key_groups.update(_file_to_key_group(path),)
+ return sorted(key_groups)
 
  def fill_metadata(self, pattern, metadata):
  pass
 
+
+def _key_group_to_entities(key_group):
+ return dict([group.split("-") for group in key_group.split("_")])
+
+
+def _entities_to_key_group(entities):
+ group_keys = sorted(entities.keys() - NON_KEY_ENTITIES)
+ return "_".join(
+ ["{}-{}".format(key, entities[key]) for key in group_keys])
+
+
+def _file_to_key_group(filename):
+ entities = parse_file_entities(str(filename))
+ return _entities_to_key_group(entities)
+
+
+def _get_param_groups(files):
+ """Finds a list of *parameter groups* from a list of files.
+
+ Parameters:
+ -----------
+
+ files : list
+ List of file names
+
+ Returns:
+ --------
+
+ parameter_groups : list
+ A list of unique parameter groups
+
+ For each file in `files`, find critical parameters for metadata. Then find
+ unique sets of these critical parameters.
+ """
+ pass

bond/testdata/complete/README

@@ -1 +1,2 @@
-Heavily downsampled CS-DSI testing datasets
+Heavily downsampled CS-DSI testing datasets.
+This dataset is valid BIDS.

bond/testdata/inconsistent/README

@@ -0,0 +1,10 @@
+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.
+
+## Changes
+
+ - sub-01_ses-phdiff_acq-HASC55AP_dwi: EchoTime set to 0.04 from 0.089
+ - sub-02_ses-phdiff_task-rest_bold: Fieldmap has been removed
+ - sub-03_ses-phdiff_task-rest_bold: FlipAngle set to 70 from 90

bond/testdata/inconsistent/dataset_description.json

@@ -0,0 +1,7 @@
+{
+ "BIDSVersion": "1.0.0",
+ "License": "BSD 3-clause",
+ "Name": "Heavily downsampled CS-DSI simulated data",
+ "ReferencesAndLinks": [],
+ "Authors": ["PennLINC", "PennBBL"]
+}

bond/testdata/inconsistent/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json

@@ -0,0 +1,33 @@
+{
+ "Manufacturer": "Siemens",
+ "ManufacturersModelName": "Prisma_fit",
+ "AcquisitionNumber": 1,
+ "InstitutionName": "HUP",
+ "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104",
+ "DeviceSerialNumber": "167024",
+ "SoftwareVersions": "syngo_MR_E11",
+ "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST",
+ "ScanningSequence": "GR_IR",
+ "SequenceVariant": "SK_SP_MP",
+ "SeriesDescription": "ABCD_T1w_MPR_vNav",
+ "BodyPartExamined": "BRAIN",
+ "ProtocolName": "ABCD_T1w_MPR_vNav",
+ "SequenceName": "tfl3d1_16ns",
+ "ImageType": [
+ "ORIGINAL",
+ "PRIMARY",
+ "M",
+ "ND",
+ "NORM"
+ ],
+ "AcquisitionTime": "16:15:31.770000",
+ "MagneticFieldStrength": 3,
+ "FlipAngle": 8,
+ "EchoTime": 0.0029,
+ "RepetitionTime": 2.5,
+ "InversionTime": 1.07,
+ "PhaseEncodingLines": 256,
+ "PhaseEncodingDirection": "i-",
+ "ConversionSoftware": "dcm2niix",
+ "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0"
+}

bond/testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval

@@ -0,0 +1 @@
+0 0 2000 3780 3800 4380 2195 2205 4200 3570 1005 2800 3790 3390 0 3605 3980 2575 3605 4195 3570 4175 3385 3395 4185 2395 4985 0 1800 1800 3780 1610 4000 4170 1190 2785 3215 200 1985 3980 0 3385 4385 4955 395 3975 3390 3965 3395 205 3385 4385 5015 990 1800 1010 1190 2605 2195 4380 0 

bond/testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec

@@ -0,0 +1,3 @@
+0 0 0.947306 -0.689491 -0.687391 -0.640236 0.904801 0.301134 0.218033 0.236237 -0.00045876 -0.267232 -0.229644 0.727918 0 -0.235344 -0.895859 0.556585 -0.235344 -0.872345 0.236237 0.218536 -0.485657 -0.969313 0.873651 0.577663 0.999993 0 -0.665829 0.665829 -0.689491 0.704677 -0.00022427 -0.437403 0.409502 0.26769 -0.00031134 0.999772 -0.00016233 0.895859 0 0.971029 0.426584 0 -0.712479 -0.00011346 -0.727918 -0.448521 -0.484877 -0.00487633 -0.485657 -0.426584 -0.00019956 -0.00045946 0.665829 -0.445079 0.409502 -0.830354 -0.904801 0.640236 0 
+0 0 -0.320301 -0.233031 0.690471 -0.429664 -0.305819 -0.906545 0.874886 0.239537 0.898412 0.804939 0.691594 0.488404 0 -0.943991 -0.00303821 -0.00388069 0.943991 -0.439269 -0.239537 0.439998 0.488955 -0.245811 0.221429 -0.581525 -0.00280889 0 0.670455 -0.670455 0.233031 -0.709514 -0.896432 0.221712 -0.414997 -0.538836 -0.999995 -0.0151408 0.32154 -0.00303821 0 -0.00329842 0.642719 -0.00262411 -0.0090312 -0.450857 0.488404 -0.00293403 -0.730564 -0.999882 -0.488955 -0.642719 -0.999997 -0.454441 0.670455 -0.895473 0.414997 -0.557225 -0.305819 -0.429664 0 
+0 0 -0.00426696 -0.685783 -0.225265 -0.636779 -0.296327 -0.295796 -0.432477 -0.941708 -0.439154 -0.529773 -0.684807 -0.481245 0 -0.231289 -0.444328 -0.830781 -0.231289 -0.214611 -0.941708 -0.871001 -0.724611 -0.00307126 -0.433248 -0.57283 -0.00260781 0 -0.327355 -0.327355 -0.685783 -0.00439859 -0.443181 -0.871506 -0.812457 -0.798748 -0.00311231 -0.0150655 -0.946896 -0.444328 0 -0.238939 -0.636348 -0.999997 -0.701635 -0.892596 -0.481245 -0.893768 -0.480802 -0.014558 -0.724611 -0.636348 -0.00259323 -0.890777 -0.327355 -0.00576167 -0.812457 -0.00362001 -0.296327 -0.636779 0 

bond/testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json

@@ -0,0 +1,75 @@
+{
+ "ProcedureStepDescription": "MR_HEAD_WO_IV_CONTRAST",
+ "DeviceSerialNumber": "167024",
+ "EffectiveEchoSpacing": 0.000689998,
+ "TotalReadoutTime": 0.0717598,
+ "ManufacturersModelName": "Prisma_fit",
+ "ProtocolName": "ABCD_dMRI",
+ "BandwidthPerPixelPhaseEncode": 10.352,
+ "PhaseEncodingLines": 140,
+ "RepetitionTime": 4.2,
+ "EchoTrainLength": 105,
+ "MagneticFieldStrength": 3,
+ "AcquisitionNumber": 1,
+ "InstitutionName": "HUP",
+ "BodyPartExamined": "BRAIN",
+ "ConversionSoftware": "dcm2niix",
+ "ScanningSequence": "EP",
+ "Manufacturer": "Siemens",
+ "FlipAngle": 90,
+ "ConversionSoftwareVersion": "v1.0.20170724 (OpenJPEG build) GCC6.1.0",
+ "SeriesDescription": "ABCD_dMRI",
+ "InstitutionAddress": "Spruce_Street_3400_Philadelphia_Pennsylvania_US_19104",
+ "AcquisitionTime": "16:31:6.145000",
+ "SequenceName": "ep_b0",
+ "ImageType": [
+ "ORIGINAL",
+ "PRIMARY",
+ "DIFFUSION",
+ "NONE",
+ "ND",
+ "MOSAIC"
+ ],
+ "EchoTime": 0.04,
+ "SequenceVariant": "SK_SP",
+ "SliceTiming": [
+ 0.0,
+ 0.11666666666666667,
+ 0.23333333333333334,
+ 0.35,
+ 0.4666666666666667,
+ 0.5833333333333334,
+ 0.7,
+ 0.8166666666666667,
+ 0.9333333333333333,
+ 1.05,
+ 1.1666666666666667,
+ 1.2833333333333334,
+ 1.4,
+ 1.5166666666666666,
+ 1.6333333333333333,
+ 1.75,
+ 1.8666666666666667,
+ 1.9833333333333334,
+ 2.1,
+ 2.216666666666667,
+ 2.3333333333333335,
+ 2.45,
+ 2.566666666666667,
+ 2.6833333333333336,
+ 2.8,
+ 2.9166666666666665,
+ 3.033333333333333,
+ 3.15,
+ 3.2666666666666666,
+ 3.3833333333333333,
+ 3.5,
+ 3.6166666666666667,
+ 3.7333333333333334,
+ 3.85,
+ 3.966666666666667,
+ 4.083333333333333
+ ],
+ "PhaseEncodingDirection": "j",
+ "SoftwareVersions": "syngo_MR_E11"
+}

bond/testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json

@@ -0,0 +1,67 @@
+{
+ "AcquisitionMatrixPE": 64,
+ "AcquisitionNumber": 1,
+ "BaseResolution": 64,
+ "BodyPartExamined": "BRAIN",
+ "ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+ "ConversionSoftware": "dcm2niix",
+ "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0",
+ "EchoTime": 0.004,
+ "FlipAngle": 60,
+ "ImageOrientationPatientDICOM": [
+ 1,
+ 0,
+ 0,
+ 0,
+ 1,
+ 0
+ ],
+ "ImageType": [
+ "ORIGINAL",
+ "PRIMARY",
+ "M",
+ "ND"
+ ],
+ "InPlanePhaseEncodingDirectionDICOM": "COL",
+ "InstitutionName": "HUP6",
+ "MRAcquisitionType": "2D",
+ "MagneticFieldStrength": 3,
+ "Manufacturer": "Siemens",
+ "ManufacturersModelName": "Prisma_fit",
+ "Modality": "MR",
+ "PartialFourier": 0.75,
+ "PatientPosition": "HFS",
+ "PercentPhaseFOV": 100,
+ "PhaseEncodingDirection": "j-",
+ "PhaseEncodingSteps": 48,
+ "PhaseResolution": 1,
+ "PixelBandwidth": 500,
+ "ProtocolName": "B0map_v4",
+ "PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping",
+ "ReceiveCoilActiveElements": "HEA;HEP",
+ "ReceiveCoilName": "Head_32",
+ "ReconMatrixPE": 64,
+ "RepetitionTime": 1.5,
+ "SAR": 0.0935879,
+ "ScanOptions": "PFP_FS",
+ "ScanningSequence": "GR",
+ "SequenceName": "_fm2d2",
+ "SequenceVariant": "SP",
+ "SeriesDescription": "B0map_v4",
+ "SeriesNumber": 7,
+ "ShimSetting": [
+ 1747,
+ -3883,
+ -285,
+ 583,
+ 125,
+ -23,
+ -45,
+ -40
+ ],
+ "SliceThickness": 4,
+ "SoftwareVersions": "syngo_MR_E11",
+ "SpacingBetweenSlices": 4,
+ "StationName": "HUP_FNDBA_MR2",
+ "TxRefAmp": 220.327
+}

bond/testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json

@@ -0,0 +1,68 @@
+{
+ "AcquisitionMatrixPE": 64,
+ "AcquisitionNumber": 1,
+ "BaseResolution": 64,
+ "BodyPartExamined": "BRAIN",
+ "ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+ "ConversionSoftware": "dcm2niix",
+ "ConversionSoftwareVersion": "v1.0.20180622 GCC6.3.0",
+ "EchoNumber": 2,
+ "EchoTime": 0.00646,
+ "FlipAngle": 60,
+ "ImageOrientationPatientDICOM": [
+ 1,
+ 0,
+ 0,
+ 0,
+ 1,
+ 0
+ ],
+ "ImageType": [
+ "ORIGINAL",
+ "PRIMARY",
+ "M",
+ "ND"
+ ],
+ "InPlanePhaseEncodingDirectionDICOM": "COL",
+ "InstitutionName": "HUP6",
+ "MRAcquisitionType": "2D",
+ "MagneticFieldStrength": 3,
+ "Manufacturer": "Siemens",
+ "ManufacturersModelName": "Prisma_fit",
+ "Modality": "MR",
+ "PartialFourier": 0.75,
+ "PatientPosition": "HFS",
+ "PercentPhaseFOV": 100,
+ "PhaseEncodingDirection": "j-",
+ "PhaseEncodingSteps": 48,
+ "PhaseResolution": 1,
+ "PixelBandwidth": 500,
+ "ProtocolName": "B0map_v4",
+ "PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping",
+ "ReceiveCoilActiveElements": "HEA;HEP",
+ "ReceiveCoilName": "Head_32",
+ "ReconMatrixPE": 64,
+ "RepetitionTime": 1.5,
+ "SAR": 0.0935879,
+ "ScanOptions": "PFP_FS",
+ "ScanningSequence": "GR",
+ "SequenceName": "_fm2d2",
+ "SequenceVariant": "SP",
+ "SeriesDescription": "B0map_v4",
+ "SeriesNumber": 7,
+ "ShimSetting": [
+ 1747,
+ -3883,
+ -285,
+ 583,
+ 125,
+ -23,
+ -45,
+ -40
+ ],
+ "SliceThickness": 4,
+ "SoftwareVersions": "syngo_MR_E11",
+ "SpacingBetweenSlices": 4,
+ "StationName": "HUP_FNDBA_MR2",
+ "TxRefAmp": 220.327
+}