add timings for tecnaiccd, improve speed test, fix safearray orientation

Author: azazellochg

pytemscript/plugins/tecnai_ccd_plugin.py

@@ -39,12 +39,18 @@ def acquire_image(self,
             #img = self.ccd_plugin.AcquireImageShown()
             #img = self.ccd_plugin.AcquireDarkSubtractedImage() # variant
 
+            t0 = time.time()
             img = self.ccd_plugin.AcquireRawImage()  # variant / tuple
+            t1 = time.time()
 
             if kwargs.get('show', False):
                 self.ccd_plugin.ShowAcquiredImage()
 
             image = convert_image(img, name=cameraName, use_safearray=False, **self._img_params)
+            t2 = time.time()
+            logging.debug("\tAcquisition took %f s" % (t1 - t0))
+            logging.debug("\tConverting image took %f s" % (t2 - t1))
+
             return image
         else:
             raise Exception("Camera is busy acquiring...")

pytemscript/utils/misc.py

@@ -132,12 +132,14 @@ def convert_image(obj,
         # Convert to a safearray and then to numpy
         from comtypes.safearray import safearray_as_ndarray
         with safearray_as_ndarray:
-            data = obj.AsSafeArray.astype("uint16")  # AsSafeArray always returns int32 array
+            # AsSafeArray always returns int32 array
+            # Also, transpose is required to match TIA orientation
+            data = obj.AsSafeArray.astype("uint16").T
 
     elif use_asfile:
         # Save into a temp file and read into numpy
         import imageio
-        fn = "C:\\temp.tif"
+        fn = r"C:/temp.tif"
         if os.path.exists(fn):
             os.remove(fn)
         obj.SaveToFile(fn) if advanced else obj.AsFile(fn, 0)

tests/test_speed.py

@@ -14,7 +14,7 @@ def acquire_image(microscope: Microscope, camera: str, **kwargs) -> Image:
 
 def main() -> None:
     """ Testing acquisition speed. """
-    microscope = Microscope(debug=True)
+    microscope = Microscope(debug=True, useTecnaiCCD=False)
 
     print("Starting acquisition speed test")
     cameras = microscope.acquisition.cameras
@@ -23,14 +23,19 @@ def main() -> None:
         if camera in cameras:
 
             print("\tUsing SafeArray")
-            acquire_image(microscope, camera)
+            img1 = acquire_image(microscope, camera)
+            img1.save(r"C:/%s_safearray.mrc" % camera, overwrite=True)
 
             print("\tUsing AsFile")
-            acquire_image(microscope, camera, use_safearray=False, use_asfile=True)
+            # This should be 3x faster than SafeArray method above
+            img2 = acquire_image(microscope, camera, use_safearray=False, use_asfile=True)
+            img2.save(r"C:/%s_asfile.mrc" % camera, overwrite=True)
 
-            if camera == "EF-CCD":
+            if camera in ["EF-CCD", "BM-Orius"]:
                 print("\tUsing TecnaiCCD/TIA")
-                acquire_image(microscope, camera, use_tecnaiccd=True)
+                # This is faster than std scripting for Gatan CCD cameras
+                img3 = acquire_image(microscope, camera, use_tecnaiccd=True)
+                img3.save(r"C:/%s_tecnaiccd.mrc" % camera, overwrite=True)
 
 
 if __name__ == '__main__':