nd2 converter names files with antibody

source/nd2converter.py

@@ -5,46 +5,58 @@ import os
 import glob
 from PIL import Image
 
-parent_dir = 'data-folder/sharepoint'
+# location of the nd2 files to convert
+parent_dir = 'data-folder/from-sharepoint/OneDrive_1_01-02-2021'
 filenames = []
+filenames_base = []
 
 for file in glob.glob(os.path.join(parent_dir, '*nd2')):
     filenames.append(file)
+
 filenames = sorted(filenames)
-print(filenames)
 
 for name in filenames:
+    base=os.path.basename(name)
+    os.path.splitext(base)
+    name_base = os.path.splitext(base)[0]
+    new_name = parent_dir+'/'+str(name_base)
+    print(new_name)
 
-    with ND2Reader(str(name)) as images:
-        plt.figure(figsize = (10,10))
-        plt.gca().set_axis_off()
-        plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
-                hspace = 0, wspace = 0)
-        plt.margins(0,0)
-        plt.gca().xaxis.set_major_locator(plt.NullLocator())
-        plt.gca().yaxis.set_major_locator(plt.NullLocator())
-        plt.imshow(images[0],cmap = 'gray')
-    ### keep metadata... e.g.
-    ## savefig(fname, dpi=None, facecolor='w', edgecolor='w',
-    ## orientation='portrait', papertype=None, format=None,
-    ## transparent=False, bbox_inches=None, pad_inches=0.1,
-    ## frameon=None, metadata=None)
-        plt.savefig(str(name)+'cells.jpeg')
-        plt.figure(figsize = (10,10))
-        plt.gca().set_axis_off()
-        plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
-            hspace = 0, wspace = 0)
-        plt.margins(0,0)
-        plt.gca().xaxis.set_major_locator(plt.NullLocator())
-        plt.gca().yaxis.set_major_locator(plt.NullLocator())
-        plt.imshow(images[1],cmap = 'gray')
-        plt.savefig(str(name)+'foci.jpeg')
-        plt.figure(figsize = (10,10))
-        plt.gca().set_axis_off()
-        plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
+    try:
+
+        with ND2Reader(str(name)) as images:
+            plt.figure(figsize = (10,10))
+            plt.gca().set_axis_off()
+            plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
+                    hspace = 0, wspace = 0)
+            plt.margins(0,0)
+            plt.gca().xaxis.set_major_locator(plt.NullLocator())
+            plt.gca().yaxis.set_major_locator(plt.NullLocator())
+            plt.imshow(images[0],cmap = 'gray')
+        ### keep metadata... e.g.
+        ## savefig(fname, dpi=None, facecolor='w', edgecolor='w',
+        ## orientation='portrait', papertype=None, format=None,
+        ## transparent=False, bbox_inches=None, pad_inches=0.1,
+        ## frameon=None, metadata=None)
+            plt.savefig(str(new_name)+'-DAPI.jpeg')
+            plt.figure(figsize = (10,10))
+            plt.gca().set_axis_off()
+            plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
                 hspace = 0, wspace = 0)
-        plt.margins(0,0)
-        plt.gca().xaxis.set_major_locator(plt.NullLocator())
-        plt.gca().yaxis.set_major_locator(plt.NullLocator())
-        plt.imshow(images[2],cmap = 'gray')
-        plt.savefig(str(name)+'dna.jpeg')
+            plt.margins(0,0)
+            plt.gca().xaxis.set_major_locator(plt.NullLocator())
+            plt.gca().yaxis.set_major_locator(plt.NullLocator())
+            plt.imshow(images[1],cmap = 'gray')
+            plt.savefig(str(new_name)+'-MLH3.jpeg')
+            plt.figure(figsize = (10,10))
+            plt.gca().set_axis_off()
+            plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0,
+                    hspace = 0, wspace = 0)
+            plt.margins(0,0)
+            plt.gca().xaxis.set_major_locator(plt.NullLocator())
+            plt.gca().yaxis.set_major_locator(plt.NullLocator())
+            plt.imshow(images[2],cmap = 'gray')
+            plt.savefig(str(new_name)+'-SYCP3.jpeg')
+
+    except:
+        print("Couldn't open file"+str(name))