correct dependencies for imwrite, imread in preprocessing routine

Author: muellerflorian

notebooks/distance-closest-object.ipynb

@@ -7,7 +7,7 @@
     "# Notebook to perform segmentation of either cells or nuclei with cellpose.\n",
     "* Requires that `cellpose` and the code of this respository are installed. One way to do this is with a pip install (recommended in a dedicated conda environment as explained in the documentation).\n",
     "   ```\n",
-    "   pip install git+https://github.com/muellerflorian/segmentation/ --upgrade\n",
+    "   pip install git+https://github.com/muellerflorian/fq-segmentation/ --upgrade\n",
     "   ```"
    ]
   },
@@ -30,18 +30,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# >> Function call\n",
+    "# >>>> Function call\n",
     "\n",
-    "# Parameters\n",
+    "# >> Parameters\n",
     "path_scan = Path(r'paste-path-to-data')            # For example data: example_data\\analysis\\segmentation-input\n",
     "\n",
     "str_label = 'mask__nuclei__'\n",
     "strs_save = ('nuclei_close_ind__', 'nuclei_close_dist__')\n",
     "truncate_distance = 255 # Distance above which distances will be truncated. \n",
     "path_save = None\n",
     "\n",
-    "\n",
-    "# Call processing function\n",
+    "# >> Call processing function\n",
     "importlib.reload(utils_masks)\n",
     "utils_masks.create_img_closest_obj(path_scan=path_scan,\n",
     "                                   str_label=str_label,\n",

notebooks/pre-processing.ipynb

@@ -8,7 +8,7 @@
     "* Takes 3D images and performs a 2D projection to obtain 2D png that can be used in the segmentation algorithm.\n",
     "* Requires that `cellpose` and the code of this respository are installed. One way to do this is with a pip install (recommended in a dedicated conda environment as explained in the documentation).\n",
     "   ```\n",
-    "   pip install git+https://github.com/muellerflorian/segmentation/ --upgrade\n",
+    "   pip install git+https://github.com/muellerflorian/fq-segmentation/ --upgrade\n",
     "   ```"
    ]
   },

segwrap/__init__.py

@@ -12,4 +12,4 @@
 # MINOR: new features
 # PATCH: backwards compatible bug fixes
 # MAJOR.MINOR.PATCHdev means a version under development
-__version__ = "0.3.2"
+__version__ = "0.3.3"

segwrap/utils_cellpose.py

@@ -9,7 +9,7 @@
 import cv2
 
 # Imports of CellPose specific libraries
-from cellpose import models, utils, io, plot
+from cellpose import models, io, plot
 from segwrap.utils_general import log_message, create_output_path
 
 # Call predict function

segwrap/utils_segmentation.py

@@ -1,8 +1,8 @@
 # Imports
 import pathlib
 import json
-from skimage.io import imread, imsave
-
+#from skimage.io import imread, imsave
+from cellpose.io import imread, imsave
 from segwrap.utils_general import log_message, create_output_path
 
 # Functions
@@ -107,7 +107,7 @@ def folder_prepare_prediction(path_process, channel_ident, img_ext, path_save, p
 
                 if name_save.is_file():
                     log_message(f'File already exists. Will be overwritten {name_save}', callback_fun=callback_log)
-                imsave(name_save, img[i, :, :])
+                imsave(str(name_save), img[i, :, :])
 
         else:
 
@@ -121,4 +121,4 @@ def folder_prepare_prediction(path_process, channel_ident, img_ext, path_save, p
 
             if name_save.is_file():
                 log_message(f'File already exists. Will be overwritten {name_save}', callback_fun=callback_log)
-            imsave(name_save, img_proj.astype('uint16'))
+            imsave(str(name_save), img_proj.astype('uint16'))