removed excessive print statements

PyNutil/coordinate_extraction.py

@@ -246,7 +246,6 @@ def load_segmentation(segmentation_path: str):
 def detect_pixel_id(segmentation: np.array):
     """Remove the background from the segmentation and return the pixel id."""
     segmentation_no_background = segmentation[~np.all(segmentation == 0, axis=2)]
-    print("length of non background pixels: ", len(segmentation_no_background))
     pixel_id = segmentation_no_background[0]
     print("detected pixel_id: ", pixel_id)
     return pixel_id

PyNutil/main.py

@@ -245,8 +245,6 @@ def quantify_coordinates(self):
         per_section_df = []
         current_centroids = None
         current_points = None
-        print("region areas list")
-        print(self.region_areas_list)
         for pl, cl, ra in zip(
             self.points_len, self.centroids_len, self.region_areas_list
         ):
@@ -257,8 +255,6 @@ def quantify_coordinates(self):
             current_df = pixel_count_per_region(
                 current_points, current_centroids, self.atlas_labels
             )
-            print("current df", current_df)
-
             # create the df for section report and all report
             # pixel_count_per_region returns a df with idx, pixel count, name and RGB.
             # ra is region area list from

PyNutil/read_and_write.py

@@ -17,7 +17,6 @@ def load_visualign_json(filename):
         slices = vafile["sections"]
         vafile["slices"] = slices
         for slice in slices:
-            print(slice)
             slice["nr"] = int(re.search(r"_s(\d+)", slice["filename"]).group(1))
             if "ouv" in slice:
                 slice["anchoring"] = slice["ouv"]
@@ -108,7 +107,6 @@ def code():
             if "SegRLEv1" != f.read(8).decode():
                 raise "Header mismatch"
             atlas = f.read(code()).decode()
-            print(f"Target atlas: {atlas}")
             codes = [code() for x in range(code())]
             w = code()
             h = code()
@@ -158,9 +156,6 @@ def files_in_directory(directory):
     list_of_files = []
     for file in os.scandir(directory):
         if file.path.endswith(".flat") and file.is_file:
-            # print(filename.path)
-            # newfilename, file_ext = os.path.splitext(filename)
-            # print(newfilename)
             filename = os.path.basename(file)
             newfilename, file_ext = os.path.splitext(filename)
             list_of_files.append(newfilename)

PyNutil/visualign_deformations.py

@@ -154,8 +154,6 @@ def __init__(self, a, b, c, vlist, elist):
         self.decomp = inv3x3(
             [[bx - ax, by - ay, 0], [cx - ax, cy - ay, 0], [ax, ay, 1]]
         )
-        if self.decomp == None:
-            print("e")
         a2 = distsquare(bx, by, cx, cy)
         b2 = distsquare(ax, ay, cx, cy)
         c2 = distsquare(ax, ay, bx, by)
@@ -211,8 +209,6 @@ def inforward_vec(self, x, y, xPrime, yPrime):
         )
 
     def intriangle_vec(self, x, y, xPrime, yPrime):
-        if self.decomp is None:
-            print("e")
         uv1 = rowmul3_vec(x, y, self.decomp)
         # also compute the next step, since it uses the parameters of this triangle
         ok = (

scripts/waln_to_json.py

@@ -16,26 +16,13 @@ def waln_to_json(filename):
         vafile["slices"] = slices 
 
         for slice in slices:
-            print(slice) # this prints info from waln to screen.
             if "filename" in slice:
                 base_name = os.path.basename(slice["filename"]).split('.')[0]
                 new_filename = base_name + '.png'
                 slice["filename"] = new_filename
             slice["nr"] = int(re.search(r"_s(\d+)", slice["filename"]).group(1))
             if "ouv" in slice:
                 slice["anchoring"] = slice["ouv"]        
-
-        '''
-        for slice in slices:
-            print(slice) # this prints info from waln to screen.
-            if "filename" in slice:
-                name, old_extension = slice["filename"].rsplit('.',1)
-                new_filename = name + '.png'
-                slice["filename"] = new_filename
-            slice["nr"] = int(re.search(r"_s(\d+)", slice["filename"]).group(1))
-            if "ouv" in slice:
-                slice["anchoring"] = slice["ouv"]
-        '''
 
         name = os.path.basename(filename)
         va_compat_file = {
@@ -51,8 +38,6 @@ def waln_to_json(filename):
             #json.dump(va_compat_file, f, indent=4) 
             json.dump(va_compat_file, f, indent=4)
 
-        print("Waln or Wwrp converted successfully to JSON")
-
     else:
         pass