Save output paths as strings

nel-lab · Jun 7, 2024 · 4c346f7 · 4c346f7
1 parent d943d7c
commit 4c346f7
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 15 deletions.
diff --git a/mesmerize_core/algorithms/cnmf.py b/mesmerize_core/algorithms/cnmf.py
@@ -7,7 +7,7 @@
 import numpy as np
 import pandas as pd
 import traceback
-from pathlib import Path
+from pathlib import Path, PurePosixPath
 from shutil import move as move_file
 import os
 import time
@@ -116,13 +116,14 @@ def run_algo(batch_path, uuid, data_path: str = None):
             Yr._mmap.close()  # accessing private attr but windows is annoying otherwise
         move_file(fname_new, cnmf_memmap_path)
 
-        cnmf_hdf5_path = output_path.relative_to(output_dir.parent)
-        cnmf_memmap_path = cnmf_memmap_path.relative_to(output_dir.parent)
-        corr_img_path = corr_img_path.relative_to(output_dir.parent)
+        # save paths as realative path strings with forward slashes
+        cnmf_hdf5_path = str(PurePosixPath(output_path.relative_to(output_dir.parent)))
+        cnmf_memmap_path = str(PurePosixPath(cnmf_memmap_path.relative_to(output_dir.parent)))
+        corr_img_path = str(PurePosixPath(corr_img_path.relative_to(output_dir.parent)))
         for proj_type in proj_paths.keys():
-            d[f"{proj_type}-projection-path"] = proj_paths[proj_type].relative_to(
+            d[f"{proj_type}-projection-path"] = str(PurePosixPath(proj_paths[proj_type].relative_to(
                 output_dir.parent
-            )
+            )))
 
         d.update(
             {

diff --git a/mesmerize_core/algorithms/cnmfe.py b/mesmerize_core/algorithms/cnmfe.py
@@ -5,7 +5,7 @@
 from caiman.source_extraction.cnmf.params import CNMFParams
 import psutil
 import traceback
-from pathlib import Path
+from pathlib import Path, PurePosixPath
 from shutil import move as move_file
 import os
 import time
@@ -107,7 +107,8 @@ def run_algo(batch_path, uuid, data_path: str = None):
             Yr._mmap.close()  # accessing private attr but windows is annoying otherwise
         move_file(fname_new, cnmf_memmap_path)
 
-        cnmfe_memmap_path = cnmf_memmap_path.relative_to(output_dir.parent)
+        # save path as realative path strings with forward slashes
+        cnmfe_memmap_path = str(PurePosixPath(cnmf_memmap_path.relative_to(output_dir.parent)))
 
         d.update(
             {

diff --git a/mesmerize_core/algorithms/mcorr.py b/mesmerize_core/algorithms/mcorr.py
@@ -7,7 +7,7 @@
 import psutil
 import pandas as pd
 import os
-from pathlib import Path
+from pathlib import Path, PurePosixPath
 import numpy as np
 from shutil import move as move_file
 import time
@@ -124,14 +124,14 @@ def run_algo(batch_path, uuid, data_path: str = None):
             shift_path = output_dir.joinpath(f"{uuid}_shifts.npy")
             np.save(str(shift_path), shifts)
 
-        # relative paths
-        cn_path = cn_path.relative_to(output_dir.parent)
-        mcorr_memmap_path = mcorr_memmap_path.relative_to(output_dir.parent)
-        shift_path = shift_path.relative_to(output_dir.parent)
+        # save paths as realative path strings with forward slashes
+        cn_path = str(PurePosixPath(cn_path.relative_to(output_dir.parent)))
+        mcorr_memmap_path = str(PurePosixPath(mcorr_memmap_path.relative_to(output_dir.parent)))
+        shift_path = str(PurePosixPath(shift_path.relative_to(output_dir.parent)))
         for proj_type in proj_paths.keys():
-            d[f"{proj_type}-projection-path"] = proj_paths[proj_type].relative_to(
+            d[f"{proj_type}-projection-path"] = str(PurePosixPath(proj_paths[proj_type].relative_to(
                 output_dir.parent
-            )
+            )))
 
         d.update(
             {