Merge pull request #472 from bids-standard/bids_website

[MAINT] update dataset listing
bids-standard · Nov 10, 2024 · 2f634a1 · 2f634a1
2 parents 38e3467 + f08050f
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diff --git a/README.md b/README.md
@@ -136,6 +136,19 @@ DO NOT EDIT DIRECTLY.
 | [asl004](https://github.com/bids-standard/bids-examples/tree/master/asl004)           | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach | anat, fmap, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
 | [asl005](https://github.com/bids-standard/bids-examples/tree/master/asl005)           | T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan                        | anat, perf       | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) |
 
+### Behavioral
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                                                        | description                                                                                 | datatypes                       | suffixes                                                                                                       | link to full data                                | maintained by                              |
+|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------|
+| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117)                             | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) |
+| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files                            | anat, beh, eeg, micr, motion    | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645)  | [@VisLab](https://github.com/VisLab)       |
+| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic)                           | A synthetic dataset                                                                         | anat, beh, func                 | T1w, beh, bold, events, physio, scans, sessions, stim                                                          | n/a                                              | [@effigies](https://github.com/effigies)   |
+
 ### EEG
 
 <!--
@@ -151,6 +164,21 @@ DO NOT EDIT DIRECTLY.
 | [eeg_matchingpennies](https://github.com/bids-standard/bids-examples/tree/master/eeg_matchingpennies)             | Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) | eeg         | channels, eeg, events                          | [link](https://doi.org/10.17605/OSF.IO/CJ2DR)   | [@sappelhoff](https://github.com/sappelhoff)   |
 | [eeg_rishikesh](https://github.com/bids-standard/bids-examples/tree/master/eeg_rishikesh)                         | Mind wandering experiment. EEG data in Biosemi (.bdf) format                                                       | eeg         | channels, eeg, events                          | [link](https://openneuro.org/datasets/ds001787) | [@arnodelorme](https://github.com/arnodelorme) |
 
+### DWI
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                                      | description                                                                                          | datatypes                       | suffixes                                                                                                       | link to full data                                              | maintained by                              |
+|:------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:-------------------------------------------|
+| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117)           | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task          | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/)               | [@RikHenson](https://github.com/RikHenson) |
+| [ds114](https://github.com/bids-standard/bids-examples/tree/master/ds114)                 | multiple tasks, multiple runs                                                                        | anat, dwi, func                 | T1w, bold, dwi, events                                                                                         | [link](https://openneuro.org/datasets/ds000114/versions/1.0.1) | n/a                                        |
+| [dwi_deriv](https://github.com/bids-standard/bids-examples/tree/master/dwi_deriv)         | exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. | dwi                             | dwi                                                                                                            | n/a                                                            | n/a                                        |
+| [eeg_rest_fmri](https://github.com/bids-standard/bids-examples/tree/master/eeg_rest_fmri) | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk)                   | anat, dwi, eeg, func            | T1w, bold, dwi, eeg                                                                                            | n/a                                                            | [@cpernet](https://github.com/cpernet)     |
+| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info                                                         | anat, dwi, func                 | FLAIR, T1w, bold, dwi, events, info                                                                            | n/a                                                            | [@cpernet](https://github.com/cpernet)     |
+
 ### iEEG
 
 <!--
@@ -167,6 +195,20 @@ DO NOT EDIT DIRECTLY.
 | [ieeg_motorMiller2007](https://github.com/bids-standard/bids-examples/tree/master/ieeg_motorMiller2007)     | Cue-based hand & tongue movement data                                                                          | ieeg                   | channels, coordsystem, electrodes, events, ieeg                        | n/a                                                                         | [@dorahermes](https://github.com/dorahermes) |
 | [ieeg_visual](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual)                       | Stimulus dependence of gamma oscillations in human visual cortex                                               | anat, ieeg             | T1w, channels, coordsystem, electrodes, events, ieeg                   | n/a                                                                         | [@dorahermes](https://github.com/dorahermes) |
 | [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a                                                                                                            | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a                                                                         | [@irisgroen](https://github.com/irisgroen)   |
+| [xeeg_hed_score](https://github.com/bids-standard/bids-examples/tree/master/xeeg_hed_score)                 | EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE                       | anat, eeg, ieeg        | T1w, channels, coordsystem, eeg, electrodes, events, ieeg              | n/a                                                                         | [@dorahermes](https://github.com/dorahermes) |
+
+### HED
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                                                              | description                                                                              | datatypes                    | suffixes                                                                                                       | link to full data                               | maintained by                                |
+|:------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:------------------------------------------------|:---------------------------------------------|
+| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo)       | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files                         | anat, beh, eeg, micr, motion | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab)         |
+| [eeg_ds003645s_hed_library](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_library) | HED annotation using HED library vocabularies (schema).                                  | eeg                          | channels, eeg, events                                                                                          | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab)         |
+| [xeeg_hed_score](https://github.com/bids-standard/bids-examples/tree/master/xeeg_hed_score)                       | EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE | anat, eeg, ieeg              | T1w, channels, coordsystem, eeg, electrodes, events, ieeg                                                      | n/a                                             | [@dorahermes](https://github.com/dorahermes) |
 
 ### MEG
 
@@ -309,16 +351,3 @@ DO NOT EDIT DIRECTLY.
 | [qmri_sa2rage](https://github.com/bids-standard/bids-examples/tree/master/qmri_sa2rage)     | Fast B1+ mapping using SA2RAGE                                                           | fmap        | TB1SRGE                                                | `not publicly available`      | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
 | [qmri_tb1tfl](https://github.com/bids-standard/bids-examples/tree/master/qmri_tb1tfl)       | B1+ mapping with TurboFLASH readout.                                                     | fmap        | TB1TFL                                                 | `not publicly available`      | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
 | [qmri_vfa](https://github.com/bids-standard/bids-examples/tree/master/qmri_vfa)             | Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. | anat, fmap  | TB1AFI, VFA                                            | [link](https://osf.io/k4bs5/) | [@agahkarakuzu](https://github.com/agahkarakuzu)             |
-
-### Behavioral
-
-<!--
-TABLE BELOW IS GENERATED AUTOMATICALLY.
-DO NOT EDIT DIRECTLY.
--->
-
-| name                                                                                                        | description                                                                                 | datatypes                       | suffixes                                                                                                       | link to full data                                | maintained by                              |
-|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------|
-| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117)                             | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) |
-| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files                            | anat, beh, eeg, micr, motion    | KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans | [link](https://openneuro.org/datasets/ds003645)  | [@VisLab](https://github.com/VisLab)       |
-| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic)                           | A synthetic dataset                                                                         | anat, beh, func                 | T1w, beh, bold, events, physio, scans, sessions, stim                                                          | n/a                                              | [@effigies](https://github.com/effigies)   |
diff --git a/dataset_listing.tsv b/dataset_listing.tsv
@@ -80,4 +80,5 @@ mrs_2dmrsi	2D sLASER MRSI data from 8 subjects	[link](https://zenodo.org/records
 mrs_biggaba	MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project	[link](https://www.nitrc.org/projects/biggaba)	[@markmikkelsen](https://github.com/markmikkelsen)	anat, mrs	T1w, mrsref, svs
 mrs_fmrs	Functional MRS data involving a pain stimulus task from 15 subjects	[link](https://www.nitrc.org/projects/fmrs_2020)	[@markmikkelsen](https://github.com/markmikkelsen)	anat, mrs	T1w, events, mrsref, svs
 2d_mb_pcasl	Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries)	[link](https://osf.io/xrkc4/)	[@aptinis](https://github.com/aptinis)	anat, fmap, perf	T1w, asl, aslcontext, epi
-xeeg_hed_score	EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE 		[@dorahermes](https://github.com/dorahermes)	eeg, anat, ieeg	channels, coordsystem, electrodes, events, ieeg, eeg, T1w
+xeeg_hed_score	EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE 		[@dorahermes](https://github.com/dorahermes)	anat, eeg, ieeg	T1w, channels, coordsystem, eeg, electrodes, events, ieeg
+dwi_deriv	exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform.			dwi	dwi
diff --git a/tools/print_dataset_listing.py b/tools/print_dataset_listing.py
@@ -4,10 +4,12 @@
 You can pass an argument to insert the content in another file.
 Otherwise the content will be added to the README of this repository.
 """
+
 import sys
 from pathlib import Path
 import pandas as pd
 from bids import BIDSLayout
+from rich import print
 
 folders_to_skip = ["docs", ".git", ".github", "tools", "env", "site", ".vscode"]
 suffixes_to_remove = ["README", "description", "participants", "CITATION"]
@@ -23,15 +25,18 @@
 UPSTREAM_REPO = "https://github.com/bids-standard/bids-examples/tree/master/"
 
 # set to True to update the listing of datasets with the datatypes and suffixes
-update_content = True
+update_content = False
 
 root = Path(__file__).resolve().parent.parent
 input_file = root / "dataset_listing.tsv"
 
 tables_order = {
     "ASL": "perf",
+    "Behavioral": "beh",
     "EEG": "^eeg$",
+    "DWI": "dwi",
     "iEEG": "ieeg",
+    "HED": "",
     "MEG": "meg",
     "Microscopy": "micr",
     "Motion": "motion",
@@ -40,11 +45,11 @@
     "NIRS": "nirs",
     "PET": "pet",
     "qMRI": "",
-    "Behavioral": "beh",
 }
 
 DELIMITER = "<!-- ADD EXAMPLE LISTING HERE -->"
 
+
 def main(output_file=None):
 
     if len(sys.argv) > 1:
@@ -55,6 +60,8 @@ def main(output_file=None):
 
     df = pd.read_csv(input_file, sep="\t")
 
+    names = df["name"].copy()
+
     check_missing_folders(df, root)
 
     if update_content:
@@ -64,12 +71,10 @@ def main(output_file=None):
 
     df = add_links(df)
 
-    print(df)
-
     clean_previous_run(output_file)
 
     df = df[column_order]
-    add_tables(df, output_file)
+    add_tables(df, output_file, names)
 
 
 def check_missing_folders(df, root):
@@ -93,10 +98,12 @@ def update_datatypes_and_suffixes(df, root):
         layout = BIDSLayout(root / row[1]["name"])
 
         tmp = sorted(layout.get_datatypes()) or ["n/a"]
+        print(f"  {tmp}")
         datatypes.append(stringify_list(tmp))
 
         tmp = layout.get_suffixes()
         tmp = sorted([s for s in tmp if s not in suffixes_to_remove]) or ["n/a"]
+        print(f"  {tmp}")
         suffixes.append(stringify_list(tmp))
 
     if not datatypes:
@@ -122,7 +129,6 @@ def add_links(df):
     return df
 
 
-
 def clean_previous_run(output_file: Path) -> None:
     print("Cleaning output files from previous run...")
     lines = output_file.read_text().split("\n")
@@ -134,28 +140,38 @@ def clean_previous_run(output_file: Path) -> None:
                 break
             f.write(line + "\n")
 
+
 def add_warning(f):
-    f.write("""<!--
+    f.write(
+        """<!--
 Table below is generated automatically.
 Do not edit directly.
 -->
 
-""".upper())
+""".upper()
+    )
+
 
-def add_tables(df: pd.DataFrame, output_file: Path) -> None:
+def add_tables(df: pd.DataFrame, output_file: Path, names) -> None:
     print("Writing markdown tables...")
     df.fillna("n/a", inplace=True)
     for table_name, table_datatypes in tables_order.items():
         with output_file.open("a") as f:
             f.write(f"\n### {table_name}\n\n")
             add_warning(f)
+
         if table_name == "qMRI":
-            sub_df = df[df["name"].str.contains("qmri_")]
+            mask = names.str.contains("qmri_")
+        elif table_name == "HED":
+            mask = names.str.contains("_hed_")
         else:
-            sub_df = df[df["datatypes"].str.contains(table_datatypes, regex=True)]
+            mask = df["datatypes"].str.contains(table_datatypes, regex=True)
+
+        sub_df = df[mask].copy()
         sub_df.sort_values(by=["name"], inplace=True)
-        # sub_df["name"] = df["name"].apply(lambda x: f'[{x}](https://github.com/bids-standard/bids-examples/tree/master/{x})')
+
         print(sub_df)
+
         sub_df.to_markdown(output_file, index=False, mode="a")
         with output_file.open("a") as f:
             f.write("\n")