sl-shared-assets 1.0.0rc10__tar.gz → 1.0.0rc11__tar.gz

{sl_shared_assets-1.0.0rc10 → sl_shared_assets-1.0.0rc11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.0.0rc10
+Version: 1.0.0rc11
 Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/

{sl_shared_assets-1.0.0rc10 → sl_shared_assets-1.0.0rc11}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "1.0.0rc10"
+version = "1.0.0rc11"
 description = "Stores assets shared between multiple Sun (NeuroAI) lab data pipelines."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-1.0.0rc10 → sl_shared_assets-1.0.0rc11}/src/sl_shared_assets/suite2p.py

@@ -52,10 +52,10 @@ class Main:
     """Determines the number of frames to process, if greater than zero. If negative (-1), the suite2p is configured
      to process all available frames."""
 
-    multiplane_parallel: bool = False
-    """Determines whether to parallelize plane processing for multiplane data. This requires a properly configured 
-    server to parallelize the computations and will not work on the local machine. Due to how suite2p is used in the 
-    lab, this has to always be set to False."""
+    multiplane_parallel: bool = True
+    """Determines whether to parallelize plane processing for multiplane data. Assuming that this configuration class is
+    used together with Sun lab optimized suite2p, it is always recommended to have this set to True for most runtimes.
+    """
 
     ignore_flyback: list[int] = field(default_factory=list)
     """The list of plane indices to ignore as flyback planes that typically contain no valid imaging data."""
@@ -162,9 +162,11 @@ class Registration:
     nimg_init: int = 500
     """The number of frames to use to compute the reference image for registration."""
 
-    batch_size: int = 1000
-    """The number of frames to register simultaneously in each batch. This depends on memory constraints. It is faster 
-    to run the registration if the batch is larger, but it requires more RAM."""
+    batch_size: int = 100
+    """The number of frames to register simultaneously in each batch. When processing data on fast (NVME) drives, 
+    increasing this parameter has minimal benefits and results in undue RAM use overhead. Therefore, on fast drives, 
+    keep this number low. On slow drives, increasing this number may result in faster runtime, at the expense of 
+    increased RAM use."""
 
     maxregshift: float = 0.1
     """The maximum allowed shift during registration, given as a fraction of the frame size, in pixels
@@ -444,6 +446,11 @@ class Suite2PConfiguration(YamlConfig):
         for section_name, section in asdict(self).items():
             # Adds all keys and values from each section to the combined dictionary
             if isinstance(section, dict):
+                # Since some keys in the original suite2p configuration file use 'unconventional' names, we opted to use
+                # conventional names in our configuration file. To make the 'ops' version of this file fully compatible
+                # with suite2p, we need to translate all such modified keys back to values expected by suite2p.
+                if "one_p_reg" in section.keys():
+                    section["1Preg"] = section.pop("one_p_reg")
                 combined_ops.update(section)
 
         return combined_ops

sl_shared_assets-1.0.0rc10/WIP.py

@@ -1,13 +0,0 @@
-from pathlib import Path
-
-from sl_shared_assets import SessionData, transfer_directory
-
-root_folder = Path("/media/Data/Experiments/Tyche")
-
-raw_data_paths = [folder for folder in root_folder.rglob("session_data.yaml")]
-
-for source in raw_data_paths:
-    sd = SessionData.load(session_path=source.parents[1], on_server=False)
-    transfer_directory(
-        source=sd.raw_data.raw_data_path, destination=sd.destinations.server_raw_data_path, verify_integrity=False
-    )