[#429] Use output_dir as file save path

oist · Apr 24, 2023 · bb6b698 · bb6b698
1 parent f695ccc
commit bb6b698
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Showing 7 changed files with 21 additions and 22 deletions.
diff --git a/optinist/api/dataclass/image.py b/optinist/api/dataclass/image.py
@@ -11,7 +11,7 @@
 
 
 class ImageData(BaseData):
-    def __init__(self, data, file_name='image'):
+    def __init__(self, data, output_dir=DIRPATH.OUTPUT_DIR, file_name='image'):
         super().__init__(file_name)
 
         self.json_path = None
@@ -23,7 +23,7 @@ def __init__(self, data, file_name='image'):
         elif isinstance(data, list) and isinstance(data[0], str):
             self.path = data
         else:
-            _dir = join_filepath([DIRPATH.OUTPUT_DIR, "tiff", file_name])
+            _dir = join_filepath([output_dir, "tiff", file_name])
             create_directory(_dir)
 
             _path = join_filepath([_dir, f'{file_name}.tif'])
@@ -49,12 +49,12 @@ def save_json(self, json_dir):
 
 
 class RoiData(BaseData):
-    def __init__(self, data, file_name='roi'):
+    def __init__(self, data, output_dir=DIRPATH.OUTPUT_DIR, file_name='roi'):
         super().__init__(file_name)
 
         images = create_images_list(data)
 
-        _dir = join_filepath([DIRPATH.OUTPUT_DIR, "tiff", file_name])
+        _dir = join_filepath([output_dir, "tiff", file_name])
         create_directory(_dir)
         self.path = join_filepath([_dir, f'{file_name}.tif'])
         tifffile.imsave(self.path, images)

diff --git a/optinist/wrappers/caiman_wrapper/cnmf.py b/optinist/wrappers/caiman_wrapper/cnmf.py
@@ -210,12 +210,12 @@ def caiman_cnmf(
     ])
 
     info = {
-        'images': ImageData(np.array(Cn * 255, dtype=np.uint8), file_name='images'),
+        'images': ImageData(np.array(Cn * 255, dtype=np.uint8), output_dir=output_dir, file_name='images'),
         'fluorescence': FluoData(fluorescence, file_name='fluorescence'),
         'iscell': IscellData(iscell, file_name='iscell'),
-        'all_roi': RoiData(all_roi, file_name='all_roi'),
-        'cell_roi': RoiData(cell_roi, file_name='cell_roi'),
-        'non_cell_roi': RoiData(non_cell_roi, file_name='non_cell_roi'),
+        'all_roi': RoiData(all_roi, output_dir=output_dir, file_name='all_roi'),
+        'cell_roi': RoiData(cell_roi, output_dir=output_dir, file_name='cell_roi'),
+        'non_cell_roi': RoiData(non_cell_roi, output_dir=output_dir, file_name='non_cell_roi'),
         'nwbfile': nwbfile
     }
 

diff --git a/optinist/wrappers/caiman_wrapper/motion_correction.py b/optinist/wrappers/caiman_wrapper/motion_correction.py
@@ -56,7 +56,7 @@ def caiman_mc(
     xy_trans_data = (np.array(mc.x_shifts_els), np.array(mc.y_shifts_els)) \
                     if params['pw_rigid'] else np.array(mc.shifts_rig)
 
-    mc_images = ImageData(images, file_name='mc_images')
+    mc_images = ImageData(images, output_dir=output_dir, file_name='mc_images')
 
     nwbfile = {}
     nwbfile[NWBDATASET.MOTION_CORRECTION] = {
@@ -68,8 +68,8 @@ def caiman_mc(
 
     info = {
         'mc_images': mc_images,
-        'meanImg': ImageData(meanImg, file_name='meanImg'),
-        'rois': RoiData(rois, file_name='rois'),
+        'meanImg': ImageData(meanImg, output_dir=output_dir, file_name='meanImg'),
+        'rois': RoiData(rois, output_dir=output_dir, file_name='rois'),
         'nwbfile': nwbfile,
     }
 

diff --git a/optinist/wrappers/lccd_wrapper/lccd_detection.py b/optinist/wrappers/lccd_wrapper/lccd_detection.py
@@ -42,7 +42,7 @@ def lccd_detect(
                 timeseries_dff[i, k] = (timeseries[i, k] - f0) / f0
 
     info = {
-        'rois': RoiData(np.nanmax(roi_list, axis=0), file_name='cell_roi'),
+        'rois': RoiData(np.nanmax(roi_list, axis=0), output_dir=output_dir, file_name='cell_roi'),
         'fluorescence': FluoData(timeseries, file_name='fluorescence'),
         'dff': FluoData(timeseries_dff, file_name='dff'),
     }

diff --git a/optinist/wrappers/suite2p_wrapper/file_convert.py b/optinist/wrappers/suite2p_wrapper/file_convert.py
@@ -1,7 +1,6 @@
 import os
 
 from optinist.api.dataclass.dataclass import *
-from optinist.api.dir_path import DIRPATH
 from optinist.api.utils.filepath_creater import join_filepath
 
 
@@ -25,7 +24,7 @@ def suite2p_file_convert(
     db = {
         'data_path': data_path_list,
         'tiff_list': data_name_list,
-        'save_path0': DIRPATH.OUTPUT_DIR,
+        'save_path0': output_dir,
         'save_folder': 'suite2p'
     }
 
@@ -40,7 +39,7 @@ def suite2p_file_convert(
     ops = io.tiff_to_binary(ops.copy())
 
     info = {
-        'meanImg': ImageData(ops['meanImg'], file_name='meanImg'),
+        'meanImg': ImageData(ops['meanImg'], output_dir=output_dir, file_name='meanImg'),
         'ops': Suite2pData(ops, file_name='ops')
     }
 

diff --git a/optinist/wrappers/suite2p_wrapper/registration.py b/optinist/wrappers/suite2p_wrapper/registration.py
@@ -25,8 +25,8 @@ def suite2p_registration(
         ops = registration.get_pc_metrics(ops)
 
     info = {
-        'refImg': ImageData(ops['refImg'], file_name='refImg'),
-        'meanImgE': ImageData(ops['meanImgE'], file_name='meanImgE'),
+        'refImg': ImageData(ops['refImg'], output_dir=output_dir, file_name='refImg'),
+        'meanImgE': ImageData(ops['meanImgE'], output_dir=output_dir, file_name='meanImgE'),
         'ops': Suite2pData(ops, file_name='ops'),
     }
 

diff --git a/optinist/wrappers/suite2p_wrapper/roi.py b/optinist/wrappers/suite2p_wrapper/roi.py
@@ -93,13 +93,13 @@ def suite2p_roi(
 
     info = {
         'ops': Suite2pData(ops),
-        'max_proj': ImageData(ops['max_proj'], file_name='max_proj'),
-        'Vcorr': ImageData(ops['Vcorr'], file_name='Vcorr'),
+        'max_proj': ImageData(ops['max_proj'], output_dir=output_dir, file_name='max_proj'),
+        'Vcorr': ImageData(ops['Vcorr'], output_dir=output_dir, file_name='Vcorr'),
         'fluorescence': FluoData(F, file_name='fluorescence'),
         'iscell': IscellData(iscell, file_name='iscell'),
-        'all_roi': RoiData(np.nanmax(im, axis=0), file_name='all_roi'),
-        'non_cell_roi': RoiData(np.nanmax(im[~iscell], axis=0), file_name='noncell_roi'),
-        'cell_roi': RoiData(np.nanmax(im[iscell], axis=0), file_name='cell_roi'),
+        'all_roi': RoiData(np.nanmax(im, axis=0), output_dir=output_dir, file_name='all_roi'),
+        'non_cell_roi': RoiData(np.nanmax(im[~iscell], axis=0), output_dir=output_dir, file_name='noncell_roi'),
+        'cell_roi': RoiData(np.nanmax(im[iscell], axis=0), output_dir=output_dir, file_name='cell_roi'),
         'nwbfile': nwbfile,
     }