some small improvmenets (#16)

README.md

@@ -71,9 +71,11 @@ Each conversion is organized in a directory of its own in the `src` directory:
         ├── clandinin_lab_to_nwb
         │   ├── conversion_directory_1
         │   └── brezovec
-        │       ├── brezovecbehaviorinterface.py
+        │       ├── brezove_convert_all_sessions.py
         │       ├── brezovec_convert_session.py
         │       ├── brezovec_metadata.yml
+        │       ├── brezovecimagingextractor.py
+        │       ├── brezovecimagininterface.py
         │       ├── brezovecnwbconverter.py
         │       ├── brezovec_requirements.txt
         │       ├── brezovec_notes.md
@@ -85,11 +87,11 @@ Each conversion is organized in a directory of its own in the `src` directory:
 
  For example, for the conversion `brezovec` you can find a directory located in `src/clandinin-lab-to-nwb/brezovec`. Inside each conversion directory you can find the following files:
 
+* `brezove_convert_all_sessions.py`: convert all the sessions.
 * `brezovec_convert_sesion.py`: this script defines the function to convert one full session of the conversion.
 * `brezovec_requirements.txt`: dependencies specific to this conversion.
 * `brezovec_metadata.yml`: metadata in yaml format for this specific conversion.
-* `brezovecbehaviorinterface.py`: the behavior interface. Usually ad-hoc for each conversion.
 * `brezovecnwbconverter.py`: the place where the `NWBConverter` class is defined.
 * `brezovec_notes.md`: notes and comments concerning this specific conversion.
-
-The directory might contain other files that are necessary for the conversion but those are the central ones.
+* `brezovecimagingextractor.py`: contains an ad-hoc imaging extractor for this conversion. This is a Bruker extractor adapted to read data from the NiFTI files used in this conversion.
+* `brezovecimagininterface.py`: the corresponding interface for the imaging extractor.

requirements.txt

@@ -1,3 +1 @@
 neuroconv
-nwbwidgets
-nwbinspector

src/clandinin_lab_to_nwb/brezovec/brezovec_convert_all_sessions.py

@@ -1,21 +1,15 @@
-from clandinin_lab_to_nwb.brezovec.brezovec_convert_session import session_to_nwb
-
-# TODO: iterate over all session
-
-# strat with:
 from pathlib import Path
-from typing import Dict
+from clandinin_lab_to_nwb.brezovec.brezovec_convert_session import session_to_nwb
 
 from neuroconv.tools.path_expansion import LocalPathExpander
 
 # Define rooth path and data directory
-root_path = Path("/media/amtra/Samsung_T5/CN_data/")
-# root_path = Path("/home/heberto/Clandinin-CN-data-share/")
+root_path = Path.home() / "Clandinin-CN-data-share"  # Change this to the directory where the data is stored
 data_dir_path = root_path / "brezovec_example_data"
-output_dir_path = root_path / "conversion_nwb"
-stub_test = True
+output_dir_path = Path.home() / "conversion_nwb"
+stub_test = False  # Set to False to convert the full session otherwise only a stub will be converted for testing
 
-# Specify source data
+# Specify source data (note this assumes the files are arranged in the same way as in the example data)
 source_data_spec = {
     "imaging_function": {
         "base_directory": data_dir_path / "imports",

src/clandinin_lab_to_nwb/brezovec/brezovec_convert_session.py

@@ -74,7 +74,9 @@ def session_to_nwb(
     prefix = f"fictrac-{session_id}"
     suffix = ".dat"
     file_path = find_items_in_directory(directory=directory, prefix=prefix, suffix=suffix)
-    source_data.update(dict(FicTrac=dict(file_path=str(file_path))))
+    diameter_mm = 9.0  # From the Brezovec paper
+    diameter_meters = diameter_mm / 1000.0
+    source_data.update(dict(FicTrac=dict(file_path=str(file_path), radius=diameter_meters / 2)))
 
     # Video
     suffix = "-raw.avi"
@@ -148,16 +150,17 @@ def session_to_nwb(
 
 
 if __name__ == "__main__":
-    # Parameters for conversion
-    root_path = Path("/media/amtra/Samsung_T5/CN_data/")
-    # root_path = Path("/home/heberto/Clandinin-CN-data-share/")
+    from pathlib import Path
+    from clandinin_lab_to_nwb.brezovec.brezovec_convert_session import session_to_nwb
+
+    root_path = Path.home() / "Clandinin-CN-data-share"  # Change this to the directory where the data is stored
     data_dir_path = root_path / "brezovec_example_data"
-    output_dir_path = root_path / "conversion_nwb"
     output_dir_path = Path.home() / "conversion_nwb"
-    stub_test = True
+    stub_test = True  # Set to False to convert the full session
     session_id = "20200620"
     subject_id = "fly2"
 
+    # Note this assumes that the files are arranged in the same way as in the example data
     session_to_nwb(
         data_dir_path=data_dir_path,
         output_dir_path=output_dir_path,

src/clandinin_lab_to_nwb/brezovec/brezovec_metadata.yaml

@@ -1,5 +1,5 @@
 NWBFile:
-  keywords: [keyword1, keyword2]
+  keywords: [walking, neural Correlates, brain-wide Scale, drosophila, volumetric two-photon imaging, neural activity mapping, locomotor signals]
   surgery: "Each fly was anesthetized on a chilled Peltier plate with a thermally coupled custom holder. Each immobilized fly was carefully fitted into a custom mount consisting of 3D-printed plastic and a custom cut steel shim to tightly nestle the head and thorax. To fix the fly to the mount, UV-curable glue was placed and cured on the dorsal region of the face between the eyes, and on the thorax. A saline solution was added to the dish for dissection (103 mM NaCl, 3 mM KCl, 5 mM TES, 1 mM NaH2PO4, 4 mM MgCl2, 1.5 mM CaCl2, 10 mM trehalose, 10 mM glucose, 7 mM sucrose, and 26 mM NaHCO3). Using a tungsten needle the posterior head cuticle was carefully cut and removed to reveal the whole brain (Figure S1). Dissection forceps were used to remove fat and trachea."
   related_publications:
     - https://doi.org/10.1101/2022.03.20.485047

src/clandinin_lab_to_nwb/brezovec/brezovec_notes.md

@@ -34,14 +34,10 @@ This is the one that was used in the experiment according to personal communicat
 [Old file organization](https://github.com/ClandininLab/brainsss2/blob/main/file_organization.md)
 
 ##  Pending questions
-* What about the rest of the subjects / sessions? We don't have them, they provide another two in the last conversion.
-* What about the video files? They are provided. Both the original and debugging.
-* What about the fictrac header? They might provided. After investigation this is not as critical as it does not contain a lot of metadata but we built in the
-machinery to read it in the data interface in neuroconv anyway.
 * Why are the bruker files not in tiff format?
-* What are the json files in the imports directory?
-* Are the nifti files pre-processed in some way (are we getting the motion corrected ones?) or are they raw? They are raw.
-* Confirm that the ANT algorithm is only applied at the population level and not at the session one. Yes, this is the most likely scenario so far.
+* Are the nifti files pre-processed in some way (are we getting the motion corrected ones?) or are they raw? Answer: They are raw.
+* Confirm that the ANT algorithm is only applied at the population level and not at the session one.
+* Synchronization data missing. Waiting for response from the authors.
 
 ## General notes
 

src/clandinin_lab_to_nwb/brezovec/brezovec_requirements.txt

@@ -1,3 +1,3 @@
-nwb-conversion-tools==0.11.1   # Example of specific pinned dependecy
-some-extra-package==1.11.3  # Example of another extra package that's necessary for the current conversion
-roiextractors @ git+https://github.com/catalystneuro/roiextractors.git@8db5f9cb3a7ee5efee49b7fd0b694c7a8105519a # Github pinned dependency
+neuroconv  # Need to pin this down when we have a release with fictrac
+roiextractors==0.5.5
+nibabel==5.1.0