Change environment and kilosort

README.md

@@ -24,10 +24,17 @@ Play around with it and raise Github issues if anything fails
    conda env create --file=processing_env.yml
    ```
 
+   For kilosorting you will also need:
+   1. Install kilosort and the GUI, run `python -m pip install kilosort[gui]`. If you're on a zsh server, you may need to use `python -m pip install "kilosort[gui]"` 
+   2. You can also just install the minimal version of kilosort with python -m pip install kilosort.
+   3. Next, if the CPU version of pytorch was installed (will happen on Windows), remove it with `pip uninstall torch`
+   4. Then install the GPU version of pytorch `conda install pytorch pytorch-cuda=11.8 -c pytorch -c nvidia`
+
    If you installed the base environment and want to update later on:
    ```shell
-   conda env --file=processing_env.yml
+   conda env update --file=processing_env.yml
    ```
+   And then do the kilosort step
 4. Create your configuration file:
    ```shell
    bnd init  # Provide the path to local and remote data storage

bnd/pipeline/kilosort.py

@@ -157,15 +157,19 @@ def run_kilosort_on_session(session_path: Path) -> None:
         logger.warning(f"Kilosort output already exists. Skipping kilosort call")
 
     else:
+        ephys_recording_folders = config.get_subdirectories_from_pattern(
+            session_path, "*_g?"
+        )
         # Check kilosort is installed in environment
         if torch.cuda.is_available():
             logger.info(f"CUDA is available. GPU device: {torch.cuda.get_device_name(0)}")
         else:
             logger.warning("CUDA is not available. GPU computations will not be enabled.")
-            return
-        ephys_recording_folders = config.get_subdirectories_from_pattern(
-            session_path, "*_g?"
-        )
+            if len(ephys_recording_folders) > 1:
+                raise ValueError(
+                    "It seems you are trying to run kilosort without GPU. Look at the README on instrucstions of how to do this. "
+                )
+
         for recording_path in ephys_recording_folders:
             logger.info(f"Processing recording: {recording_path.name}")
             run_kilosort_on_recording(

bnd/pipeline/nwb.py

@@ -116,7 +116,7 @@ def run_nwb_conversion(session_path: Path, kilosort_flag: bool, custom_map: bool
             .strip()
             .lower()
         )
-        if response != "y":
+        if "y" not in response:
             logger.warning(f"Aborting nwb conversion")
             return
         else:

bnd/pipeline/pyaldata.py

@@ -857,12 +857,12 @@ def save(self):
                     .lower()
                     .strip()
                 )
-                if user_input == "y":
+                if "y" in user_input:
                     self._partition_and_save_to_mat()
                     logger.info("Session has been overwritten.")
                     break
 
-                elif user_input == "n":
+                elif "n" in user_input:
                     logger.info("Session was not overwritten.")
                     break
 

processing_env.yml

@@ -9,15 +9,12 @@ dependencies:
   - python=3.10
   - pytest
   - typer
-  - pytorch
-  - pytorch-cuda=11.8
   - pynwb
   - numpy
   - pandas
   - scipy
   - spikeinterface
   - pip:
-      - kilosort
       - ndx_pose
       - neuroconv
       - -e ./