[ENH] Update config to support microscopy, qMRI, PET, ASL

.gitignore

@@ -1,6 +1,8 @@
 historical/
 
-#
+# clone of bids-example repo for testing
+bids/tests/data/bids-examples
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -86,6 +88,9 @@ celerybeat-schedule
 venv/
 ENV/
 
+# Pipenv
+Pipfile
+
 # Spyder project settings
 .spyderproject
 

Makefile

@@ -1,10 +1,13 @@
 .PHONY: doc tutorial travis_tests
 
-ci_tests:
+ci_tests: bids/tests/data/bids-examples
 	pytest --doctest-modules -n 2 -v --cov bids --cov-config .coveragerc --cov-report xml:cov.xml bids
 
 tutorial:
 	jupyter nbconvert --execute examples/pybids_tutorial.ipynb --to html
 
 doc:
 	$(MAKE) -C doc html
+
+bids/tests/data/bids-examples:
+	git clone https://github.com/bids-standard/bids-examples.git --depth 1 bids/tests/data/bids-examples

bids/layout/config/bids-nodot.json

@@ -12,6 +12,10 @@
             "mandatory": false,
             "directory": "{subject}{session}"
         },
+        {
+            "name": "sample",
+            "pattern": "[_/\\\\]+sample-([a-zA-Z0-9]+)"
+        },
         {
             "name": "task",
             "pattern": "[_/\\\\]+task-([a-zA-Z0-9]+)"
@@ -24,6 +28,14 @@
             "name": "ceagent",
             "pattern": "[_/\\\\]+ce-([a-zA-Z0-9]+)"
         },
+        {
+            "name": "staining",
+            "pattern": "[_/\\\\]+stain-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "tracer",
+            "pattern": "[_/\\\\]+stain-([a-zA-Z0-9]+)"
+        },
         {
             "name": "reconstruction",
             "pattern": "[_/\\\\]+rec-([a-zA-Z0-9]+)"
@@ -73,6 +85,10 @@
             "name": "space",
             "pattern": "[_/\\\\]+space-([a-zA-Z0-9]+)"
         },
+        {
+            "name": "chunk",
+            "pattern": "[_/\\\\]+chunk-([0-9]+)"
+        },
         {
             "name": "suffix",
             "pattern": "[._]*([a-zA-Z0-9]*?)\\.[^/\\\\]+$"
@@ -87,7 +103,7 @@
         },
         {
             "name": "datatype",
-            "pattern": "[/\\\\]+(func|anat|fmap|dwi|meg|eeg)[/\\\\]+"
+            "pattern": "[/\\\\]+(anat|beh|dwi|eeg|fmap|func|ieeg|meg|micr|perf|pet)[/\\\\]+"
         },
         {
             "name": "extension",
@@ -98,9 +114,9 @@
     "default_path_patterns": [
         "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_part-{part}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}.{extension<nii|nii.gz|json>|nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}.{extension<nii|nii.gz|json>|nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}.{extension<nii|nii.gz|json>|nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<phase>}.{extension<nii|nii.gz|json>|nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_part-{part}]_{suffix<dwi>}.{extension<.bval|.bvec|json|nii.gz|nii>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}]_{suffix<phase>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_part-{part}]_{suffix<dwi>}.{extension<bval|bvec|json|nii.gz|nii>|nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{fmap<phasediff|magnitude[12]|phase[12]|fieldmap>}.{extension<nii|nii.gz|json>|nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{fmap<epi>}.{extension<nii|nii.gz|json>|nii.gz}",
         "sub-{subject}[/ses-{session}]/[{datatype<func|meg|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}.{extension<tsv|json>|tsv}",
@@ -109,13 +125,45 @@
         "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_proc-{proc}]_{suffix<channels>}.{extension<tsv|json>|tsv}",
         "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}]_{suffix<coordsystem>}.{extension<json>|json}",
         "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}]_{suffix<photo>}.{extension<jpg>|jpg}",
+        "sub-{subject}/[ses-{session}]/{datatype<micr>}|micr/sub-{subject}[_ses-{session}]_sample-{sample}[_acq-{acquisition}][_stain-{label}][_run-{run}][_chunk-{index}]_{suffix<TEM|SEM|uCT|BF|DF|PC|DIC|FLUO|CONF|PLI|CARS|2PE|MPE|SR|NLO|OCT|SPIM>}.{extension<png|tif|ome.tif|ome.btf|json>}",
+        "sub-{subject}/[ses-{session}]/{datatype<micr>}|micr/sub-{subject}[_ses-{session}]_sample-{sample}[_acq-{acquisition}]_photo<extension<jpg|png|tif|json>",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_echo-{echo}[_part-{<mag|phase|real|imag>}]_{suffix<MEGRE|MESE>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}][_echo-{echo}]_flip-{flip}[_part-{<mag|phase|real|imag>}]_{suffix<VFA>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_inv-{inv}[_part-{<mag|phase|real|imag>}]_{suffix<IRT1>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}][_echo-{echo}][_flip-{flip}]_inv-{inv}[_part-{<mag|phase|real|imag>}]_{suffix<MP2RAGE>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}][_echo-{echo}]_flip-{flip}_mt-{on|off}[_part-{<mag|phase|real|imag>}]_{suffix<MPM|MTS>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_mt-{on|off}[_part-{<mag|phase|real|imag>}]_{suffix<MTR>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}/[ses-{session}]/{datatype<anat>}|anat/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_{suffix<T1map|T2map|T2starmap|R1map|R2map|R2starmap|PDmap|MTRmap|MTsat|UNIT1|T1rho|MWFmap|MTVmap|PDT2map|Chimap|S0map|M0map>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<pet>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}]_recording-{recording}_{suffix<blood>}.{extension<tsv|json>}",
+        "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}]_task-{task}[trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<events>}.{extension<tsv|json>}",
+        "sub-{subject}[/ses-{session}]/{datatype<pet>|pet}/sub-{subject}[_ses-{session}][_task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}.{extension<tsv.gz|json>}",      
+        "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir{direction}][_run-{run}]_{suffix<asl|m0scan>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir{direction}][_run-{run}]_{suffix<aslcontext>}.{extension<tsv|json>}",
+        "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_run-{run}]_{suffix<asllabeling>}.{extension<jpg>}",
+        "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir{direction}][_run-{run}][_recording{recording}]_{suffix<physio|stim>}.{extension<tsv|json>}",  
         "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_]{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}.{extension<json>|json}",
         "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][mod-{modality}_]{suffix<defacemask>}.{extension<json>|json}",
         "task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}.{extension<json>|json}",
         "[acq-{acquisition}_]{suffix<dwi>}.{extension<json>|json}",
         "[acq-{acquisition}_][dir-{direction}_][run-{run}_]{fmap<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}.{extension<json>|json}",
         "[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}]_{fmap<epi>}.{extension<json>|json}",
         "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}.{extension<json>|json}",
-        "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}.{extension<json>}"
+        "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}.{extension<json>}",
+        "sample-{sample}[_acq-{acquisition}][_stain-{label}][_run-{run}][_chunk-{index}]_{suffix<TEM|SEM|uCT|BF|DF|PC|DIC|FLUO|CONF|PLI|CARS|2PE|MPE|SR|NLO|OCT|SPIM>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_echo-{echo}[_part-{<mag|phase|real|imag>}]_{suffix<MEGRE|MESE>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}][_echo-{echo}]_flip-{flip}[_part-{<mag|phase|real|imag>}]_{suffix<VFA>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_inv-{inv}[_part-{<mag|phase|real|imag>}]_{suffix<IRT1>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}][_echo-{echo}][_flip-{flip}]_inv-{inv}[_part-{<mag|phase|real|imag>}]_{suffix<MP2RAGE>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}][_echo-{echo}]_flip-{flip}_mt-{on|off}[_part-{<mag|phase|real|imag>}]_{suffix<MPM|MTS>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_mt-{on|off}[_part-{<mag|phase|real|imag>}]_{suffix<MTR>}.{extension<json>|json}",
+        "[acq-{acquisition}][_ce-{ceagent}][_rec-{label}][_run-{run}]_{suffix<T1map|T2map|T2starmap|R1map|R2map|R2starmap|PDmap|MTRmap|MTsat|UNIT1|T1rho|MWFmap|MTVmap|PDT2map|Chimap|S0map|M0map>}.{extension<json>|json}",
+        "[task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<pet>}.{extension<json>|json}",
+        "[task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}]_recording-{recording}_{suffix<blood>}.{extension<json>|json}",
+        "task-{task}[trc-{tracer}][_rec-{reconstruction}][_run-{run}]_{suffix<events>}.{extension<json>|json}",
+        "[task-{task}][trc-{tracer}][_rec-{reconstruction}][_run-{run}][_recording-{recording}]_{suffix<physio|stim>}.{extension<json>|json}",      
+        "[acq-{acquisition}][_rec-{reconstruction}][_dir{direction}][_run-{run}]_{suffix<asl|m0scan>}.{extension<json>|json}",
+        "[acq-{acquisition}][_rec-{reconstruction}][_dir{direction}][_run-{run}]_{suffix<aslcontext>}.{extension<json>|json}",
+        "[acq-{acquisition}][_rec-{reconstruction}][_dir{direction}][_run-{run}][_recording{recording}]_{suffix<physio|stim>}.{extension<json>|json}"
     ]
 }