Merge pull request #164 from ttngu207/main

bugfix in `infer_output_dir`
datajoint · Feb 1, 2024 · 2480906 · 2480906
2 parents b6b4b69 + e514ff7
commit 2480906
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Showing 3 changed files with 6 additions and 17 deletions.
diff --git a/element_calcium_imaging/imaging.py b/element_calcium_imaging/imaging.py
@@ -254,13 +254,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
                 e.g.: sub4/sess1/scan0/suite2p_0
         """
         acq_software = (scan.Scan & key).fetch1("acq_software")
-        filetypes = dict(
-            ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
-        )
-
         scan_dir = find_full_path(
             get_imaging_root_data_dir(),
-            get_calcium_imaging_files(key, filetypes[acq_software])[0],
+            get_calcium_imaging_files(key, acq_software)[0],
         ).parent
         root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)
 

diff --git a/element_calcium_imaging/imaging_no_curation.py b/element_calcium_imaging/imaging_no_curation.py
@@ -254,13 +254,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
                 e.g.: sub4/sess1/scan0/suite2p_0
         """
         acq_software = (scan.Scan & key).fetch1("acq_software")
-        filetypes = dict(
-            ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
-        )
-
         scan_dir = find_full_path(
             get_imaging_root_data_dir(),
-            get_calcium_imaging_files(key, filetypes[acq_software])[0],
+            get_calcium_imaging_files(key, acq_software)[0],
         ).parent
         root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)
 
@@ -369,6 +365,7 @@ def make(self, key):
         task_mode, output_dir = (ProcessingTask & key).fetch1(
             "task_mode", "processing_output_dir"
         )
+        acq_software = (scan.Scan & key).fetch1("acq_software")
 
         if not output_dir:
             output_dir = ProcessingTask.infer_output_dir(key, relative=True, mkdir=True)
@@ -452,8 +449,8 @@ def make(self, key):
                         "Caiman pipeline is not yet capable of analyzing 3D scans."
                     )
 
-                # handle multi-channel tiff image before running CaImAn
-                if nchannels > 1:
+                if acq_software == "ScanImage" and nchannels > 1:
+                    # handle multi-channel tiff image before running CaImAn
                     channel_idx = caiman_params.get("channel_to_process", 0)
                     tmp_dir = pathlib.Path(output_dir) / "channel_separated_tif"
                     tmp_dir.mkdir(exist_ok=True)

diff --git a/element_calcium_imaging/imaging_preprocess.py b/element_calcium_imaging/imaging_preprocess.py
@@ -444,13 +444,9 @@ def infer_output_dir(cls, key, relative=False, mkdir=False):
                 e.g.: sub4/sess1/scan0/suite2p_0
         """
         acq_software = (scan.Scan & key).fetch1("acq_software")
-        filetypes = dict(
-            ScanImage="*.tif", Scanbox="*.sbx", NIS="*.nd2", PrairieView="*.tif"
-        )
-
         scan_dir = find_full_path(
             get_imaging_root_data_dir(),
-            get_calcium_imaging_files(key, filetypes[acq_software])[0],
+            get_calcium_imaging_files(key, acq_software)[0],
         ).parent
         root_dir = find_root_directory(get_imaging_root_data_dir(), scan_dir)