edit notebook

d33bs · Dec 9, 2022 · 3a928d2 · 3a928d2
1 parent da69b4e
commit 3a928d2
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/0_download_data/correct_images.ipynb b/0_download_data/correct_images.ipynb
@@ -40,9 +40,7 @@
    "source": [
     "path_to_pipeline = \"/home/jenna/NF1_SchwannCell_data/0_download_data/convert_crop_NF1_images.cppipe\"\n",
     "path_to_output = \"/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate_Corrected\"\n",
-    "path_to_images = \"/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate\"\n",
-    "\n",
-    "output_folder_name = \"NF1_Second_Plate_Corrected\""
+    "path_to_images = \"/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate\""
    ]
   },
   {
@@ -84,7 +82,7 @@
     }
    ],
    "source": [
-    "images_path = pathlib.Path(\"/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate_Corrected\")\n",
+    "images_path = pathlib.Path(path_to_output)\n",
     "output_folder_name = 'NF1_Second_Plate_Corrected'\n",
     "\n",
     "correct.rename_images(images_path, output_folder_name)"

diff --git a/0_download_data/correct_images.py b/0_download_data/correct_images.py
@@ -22,8 +22,6 @@
 path_to_output = "/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate_Corrected"
 path_to_images = "/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate"
 
-output_folder_name = "NF1_Second_Plate_Corrected"
-
 
 # ### Run CellProfiler to convert and crop images and reformat the metadata
 
@@ -36,7 +34,7 @@
 # In[4]:
 
 
-images_path = pathlib.Path("/home/jenna/NF1_SchwannCell_data/0_download_data/NF1_Second_Plate_Corrected")
+images_path = pathlib.Path(path_to_output)
 output_folder_name = 'NF1_Second_Plate_Corrected'
 
 correct.rename_images(images_path, output_folder_name)