explicit converting tif images to mode "I"

mtor/gui.py

@@ -217,30 +217,37 @@ class MtorImageAnalysis(QWidget):
 
 
 def run_gui():
-    app = QApplication(sys.argv)
+    import traceback
-    mia = MtorImageAnalysis()
+
-    app.exec_()
+    try:
-
+
-    if mia.analysis_parameters is not None:
+        app = QApplication(sys.argv)
-        pw = prescan_workflow(**mia.analysis_parameters)
+        mia = MtorImageAnalysis()
-        iw = image_workflow(pw.parameters)
+        app.exec_()
-        dw = data_workflow(iw.data, iw.parameters)
+
-        fw = postprocessing_workflow(dw.data, dw.parameters)
+        if mia.analysis_parameters is not None:
-        pdf_path = fw.parameters.data_dir / "report.pdf"
+            pw = prescan_workflow(**mia.analysis_parameters)
-        if sys.platform.startswith("win"):
+            iw = image_workflow(pw.parameters)
-            os.startfile(str(pdf_path))
+            dw = data_workflow(iw.data, iw.parameters)
-        else:
+            fw = postprocessing_workflow(dw.data, dw.parameters)
-            if sys.platform.startswith("darwin"):
+            pdf_path = fw.parameters.data_dir / "report.pdf"
-                cmd = ["open", str(pdf_path)]
+            if sys.platform.startswith("win"):
+                os.startfile(str(pdf_path))
             else:
-                cmd = ["xdg-open", str(pdf_path)]
+                if sys.platform.startswith("darwin"):
-            Popen(
+                    cmd = ["open", str(pdf_path)]
-                cmd,
+                else:
-                shell=False,
+                    cmd = ["xdg-open", str(pdf_path)]
-                stdin=None,
+                Popen(
-                stdout=None,
+                    cmd,
-                stderr=None,
+                    shell=False,
-                close_fds=True,
+                    stdin=None,
-            )
+                    stdout=None,
-
+                    stderr=None,
-    sys.exit()
+                    close_fds=True,
+                )
+    except Exception as err:
+        traceback.print_exc()
+        input("Press enter to close this window")
+    finally:
+        sys.exit()

mtor/imageproc.py

@@ -12,7 +12,7 @@ from .commons import (
 
 def open_as_array(tif_image):
     with tif_image.path.open("rb") as filehandle:
-        image = Image.open(filehandle)
+        image = Image.open(filehandle).convert(mode="I")
         image_array = numpy.array(image, dtype=numpy.int32)
     return TifArray(
         path=tif_image.path, frame=tif_image.frame, data=image_array

mtor/prescan.py

@@ -11,7 +11,7 @@ def scan_tifs(parameters):
 
     for tif in tqdm(parameters.tif_list):
         with tif.path.open("rb") as filehandle:
-            image = Image.open(filehandle)
+            image = Image.open(filehandle).convert(mode="I")
             mi, ma = image.getextrema()
             lowest = min(lowest, mi)
             highest = max(highest, ma)