Merge pull request #35 from stuwilkins/fix_vivek

Fix Vivek's Additions

csxtools/utils.py

@@ -12,8 +12,7 @@
 
 
 def get_fastccd_images(light_header, dark_headers=None,
-                       flat=None, gain=(1, 4, 8), tag=None,
-                       roi=None):
+                       flat=None, gain=(1, 4, 8), tag=None, roi=None):
     """Retreive and correct FastCCD Images from associated headers
 
     Retrieve FastCCD Images from databroker and correct for:
@@ -49,8 +48,8 @@ def get_fastccd_images(light_header, dark_headers=None,
         the settings.
 
     roi : tuple
-        tuple with 4 integers to crop images
-        (row_start, column_start, row_end, column_end)
+        coordinates of the upper-left corner and width and height of
+        the ROI: e.g., (x, y, w, h)
 
     Returns
     -------
@@ -61,6 +60,14 @@ def get_fastccd_images(light_header, dark_headers=None,
     if tag is None:
         tag = detectors['fccd']
 
+    # Now lets sort out the ROI
+    if roi is not None:
+        roi = list(roi)
+        # Convert ROI to start:stop from start:size
+        roi[2] = roi[0] + roi[2]
+        roi[3] = roi[1] + roi[3]
+        logger.info("Computing with ROI of %s", str(roi))
+
     if dark_headers is None:
         bgnd = None
         logger.warning("Processing without dark images")
@@ -107,9 +114,9 @@ def get_fastccd_images(light_header, dark_headers=None,
 
     # Ok, so lets return a pims pipeline which does the image conversion
 
-    # Crop Flat image
+    # Crop Flatfield image
     if flat is not None and roi is not None:
-        flat = crop_flat(flat, roi)
+        flat = _crop(flat, roi)
 
     return _correct_fccd_images(events, bgnd, flat, gain)
 
@@ -138,49 +145,32 @@ def get_images_to_4D(images, dtype=None):
     return im
 
 
-def get_images_to_3D(images):
-    """Return a 3D array from the "slicerator" object
-
-    Parameters
-    ----------
-    slicerator object : generator returning pims images
-        This is the output of get_fastccd_images
-
-    Returns
-    -------
-    array: 3D numpy array
-    """
-
-    ims = images[0]
-    for im in images[1:]:
-        ims = np.vstack((ims, im))
-
-    return ims
-
-
-@pipeline
-def _correct_fccd_images(image, bgnd, flat, gain):
-    return rotate90(correct_images(image, bgnd, flat, gain), 'cw')
-
-
 def _get_images(header, tag, roi=None):
     t = ttime.time()
     images = get_images(header, tag)
     t = ttime.time() - t
     logger.info("Took %.3f seconds to read data using get_images", t)
 
     if roi is not None:
-        return crop(images, roi)
+        images = _crop_images(images, roi)
+
     return images
 
 
 @pipeline
-def crop(image, roi=None):
-    # Assuming ROI is specified in the "rotated" (correct) orientation
-    roi = [960-roi[3], roi[0], 960-roi[1], roi[2]]
-    return image[:, roi[0]:roi[2], roi[1]:roi[3]]
+def _correct_fccd_images(image, bgnd, flat, gain):
+    image = correct_images(image, bgnd, flat, gain)
+    image = rotate90(image, 'cw')
+    return image
+
+
+@pipeline
+def _crop_images(image, roi):
+    return _crop(image, roi)
 
 
-def crop_flat(image, roi=None):
-    roi = [960-roi[3], roi[0], 960-roi[1], roi[2]]
-    return image[roi[0]:roi[2], roi[1]:roi[3]]
+def _crop(image, roi):
+    image_shape = image.shape
+    # Assuming ROI is specified in the "rotated" (correct) orientation
+    roi = [image_shape[-2]-roi[3], roi[0], image_shape[-1]-roi[1], roi[2]]
+    return image.T[roi[1]:roi[3], roi[0]:roi[2]].T