Merge pull request #43 from klemengit/master

Bug fix (get_frames)

Author: klemengit

docs/source/code/modules.rst

@@ -1,35 +1,32 @@
 pyIDI source code
 =================
 
-pyIDI base class
-----------------
-.. autoclass:: pyidi.pyidi_legacy.pyIDI
-    :members:
-
+Video Reader
+------------
 
-Displacement identification methods
------------------------------------
+.. automodule:: pyidi.video_reader
+    :members:
 
 IDIMetod base class
-^^^^^^^^^^^^^^^^^^^
+-------------------
 
 .. automodule:: pyidi.methods.idi_method
     :members:
 
 Simplified optical flow
-^^^^^^^^^^^^^^^^^^^^^^^
+-----------------------
 
 .. automodule:: pyidi.methods._simplified_optical_flow
     :members:
 
 The Lucas-Kanade algorithm for translations
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+-------------------------------------------
 
 .. automodule:: pyidi.methods._lucas_kanade
     :members:
 
 Directional Lucas-Kanade
-^^^^^^^^^^^^^^^^^^^^^^^^
+------------------------
 
 .. automodule:: pyidi.methods._directional_lucas_kanade
     :members:
@@ -40,8 +37,8 @@ Postprocessing
 .. automodule:: pyidi.postprocessing._motion_magnification
     :members:
 
-Video Reader
-------------
+pyIDI base class
+----------------
 
-.. automodule:: pyidi.video_reader
+.. autoclass:: pyidi.pyidi_legacy.pyIDI
     :members:

docs/source/conf.py

@@ -104,7 +104,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

pyidi/methods/idi_method.py

@@ -114,7 +114,10 @@ def create_temp_files(self, init_multi=False):
                     f'disp_shape: {(self.points.shape[0], self.N_time_points, 2)}\n',
                     f'analysis_run <{self.analysis_run}>:'
                 ])
-
+            
+            if not self.points.shape[0]:
+                raise Exception("Points not set. Please set the points before running the analysis.")
+            
             self.temp_disp = np.memmap(self.disp_filename, dtype=np.float64, mode='w+', shape=(self.points.shape[0], self.N_time_points, 2))
 
     def clear_temp_files(self):

pyidi/video_reader.py

@@ -164,21 +164,29 @@ def get_frames(self, frame_range=None, *args, **kwargs):
 
         if type(frame_range) in [list, tuple] and len(frame_range) != 2:
             raise ValueError('Length of the frame range must be 2!')
+        
+        if frame_range is None:
+            frames_start = 0
+            frames_end = self.N + 1
+            n_frames = self.N
+        elif type(frame_range) is int:
+            frames_start = 0
+            frames_end = frame_range
+            n_frames = frame_range
+        elif type(frame_range) in [list, tuple]:
+            frames_start = frame_range[0]
+            frames_end = frame_range[1]
+            n_frames = frame_range[1] - frame_range[0]
 
         if self.file_format in PHORTRON_HEADER_FILE or self.file_format == 'np.ndarray':
-            frames = self._frames
+            frames = self._frames[frames_start:frames_end]
 
         else:
-            frames = np.zeros((self.N, self.image_height, self.image_width))
-            for i in self.N:
-                frames[i] = self.get_frame(i, *args, **kwargs)
+            frames = np.zeros((n_frames, self.image_height, self.image_width), dtype=int)
+            for i in range(n_frames):
+                frames[i] = self.get_frame(i+frames_start, *args, **kwargs)
 
-        if frame_range is None:
-            return frames
-        elif type(frame_range) is int:
-            return frames[:frame_range]
-        elif type(frame_range) in [list, tuple]:
-            return frames[frame_range[0]:frame_range[1]]
+        return frames
 
     def _get_frame_from_image(self, frame_number, use_channel='Y'):
         """Reads the frame from the image stream, or image file containing multiple images. 

tests/test_reader/test_reader.py

@@ -13,3 +13,18 @@ def test_1():
     assert hasattr(video, "N")
     assert hasattr(video, "image_width")
     assert hasattr(video, "image_height")
+    assert hasattr(video, "fps")
+
+def test_get_frames():
+    video = pyidi.VideoReader(input_file='./data/data_synthetic_img_0.png')
+
+    assert video.get_frames().shape[0] == 10
+    assert video.get_frames(4).shape[0] == 4
+    assert video.get_frames((1, 5)).shape[0] == 4
+
+def test_get_frames_mraw():
+    video = pyidi.VideoReader(input_file='./data/data_showcase.cih')
+
+    assert video.get_frames().shape[0] == 75
+    assert video.get_frames(4).shape[0] == 4
+    assert video.get_frames((1, 5)).shape[0] == 4