tranformation fix to separate the previous implicit image orientation in pixel sign values

analysis/database.py

@@ -44,7 +44,7 @@ class DataBaseWindow(QtWidgets.QMainWindow):
         self.path = os.path.join(Path.home(), 'gepard', 'databases')
         self.importPath = self.path
         if not os.path.exists(self.path):
-            os.mkdir(self.path)
+            os.makedirs(self.path)
         self.activeDatabase = None
         self.activeSpectrum = None
         self.activeSpectrumName = None

helperfunctions.py

@@ -23,7 +23,16 @@ import numpy as np
 import cv2
 import os
 
+try:
+    from skimage.io import imread as skimread
+    from skimage.io import imsave as skimsave
+except ImportError:
+    skimread = None
+    skimsave = None
+
 def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
+    if skimread is not None:
+        return skimread(fname, as_gray=(flags==cv2.IMREAD_GRAYSCALE))
     with open(fname, "rb") as fp:
         cont = fp.read()
         img = cv2.imdecode(np.fromstring(cont, dtype=np.uint8), flags)
@@ -31,6 +40,8 @@ def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
     return None
 
 def cv2imwrite_fix(fname, img, params=None):
+    if skimsave is not None:
+        skimsave(fname, img)
     pathname, ext = os.path.splitext(fname)
     if params is None:
         ret, data = cv2.imencode(ext, img)