wip

derotation/analysis/full_rotation_pipeline.py

@@ -15,7 +15,7 @@
 from sklearn.mixture import GaussianMixture
 from tifffile import imsave
 
-from derotation.derotate_by_line import rotate_an_image_array_line_by_line
+from derotation.derotate_by_line_plot import rotate_an_image_array_line_by_line
 from derotation.load_data.custom_data_loaders import (
     get_analog_signals,
     read_randomized_stim_table,
@@ -55,7 +55,7 @@ def __call__(self):
         - adding a circular mask to the rotated image stack
         - saving the masked image stack
         """
-        self.contrast_enhancement()
+        # self.contrast_enhancement()
         self.process_analog_signals()
         rotated_images = self.rotate_frames_line_by_line()
         masked = self.add_circle_mask(rotated_images, self.mask_diameter)
@@ -236,18 +236,29 @@ def process_analog_signals(self):
         )
         self.rotation_on = self.create_signed_rotation_array()
 
-        self.drop_ticks_outside_of_rotation()
+        if self.adjust_increment:
+            self.drop_ticks_outside_of_rotation()
+            self.check_number_of_rotations()
 
-        self.check_number_of_rotations()
-        if not self.is_number_of_ticks_correct() and self.adjust_increment:
-            (
-                self.corrected_increments,
-                self.ticks_per_rotation,
-            ) = self.adjust_rotation_increment()
+            if not self.is_number_of_ticks_correct():
+                (
+                    self.corrected_increments,
+                    self.ticks_per_rotation,
+                ) = self.adjust_rotation_increment()
+        else:
+            self.corrected_increments = [
+                self.rotation_increment
+            ] * self.number_of_rotations
+            self.ticks_per_rotation = (
+                self.rot_deg
+                * self.rotation_increment
+                * self.number_of_rotations
+            )
 
         self.interpolated_angles = self.get_interpolated_angles()
 
-        self.remove_artifacts_from_interpolated_angles()
+        if self.adjust_increment:
+            self.remove_artifacts_from_interpolated_angles()
 
         (
             self.line_start,
@@ -419,7 +430,7 @@ def drop_ticks_outside_of_rotation(self) -> np.ndarray:
 
         inter_roatation_interval = [
             idx
-            for i in range(self.number_of_rotations + 1)
+            for i in range(len(edited_ends))
             for idx in range(
                 edited_ends[i],
                 rolled_starts[i],
@@ -457,8 +468,8 @@ def check_number_of_rotations(self):
             raise ValueError(
                 "Start and end of rotations have different lengths"
             )
-        if self.rot_blocks_idx["start"].shape[0] != self.number_of_rotations:
-            raise ValueError("Number of rotations is not as expected")
+        # if self.rot_blocks_idx["start"].shape[0] != self.number_of_rotations:
+        #     raise ValueError("Number of rotations is not as expected")
 
         logging.info("Number of rotations is as expected")
 
@@ -550,7 +561,7 @@ def get_interpolated_angles(self) -> np.ndarray:
 
         ticks_with_increment = [
             item
-            for i in range(self.number_of_rotations)
+            for i in range(len(self.corrected_increments))
             for item in [self.corrected_increments[i]]
             * self.ticks_per_rotation[i]
         ]
@@ -599,7 +610,7 @@ def remove_artifacts_from_interpolated_angles(self):
         rotation_end = np.where(np.diff(thresholded) < 0)[0]
 
         assert len(rotation_start) == len(rotation_end)
-        assert len(rotation_start) == self.number_of_rotations
+        # assert len(rotation_start) == self.number_of_rotations
 
         for i, (start, end) in enumerate(
             zip(rotation_start[1:], rotation_end[:-1])

derotation/analysis/incremental_rotation_pipeline.py

@@ -36,7 +36,7 @@ def __call__(self):
         After processing the analog signals, the image stack is rotated by
         frame and then registered using phase cross correlation.
         """
-        self.contrast_enhancement()
+        # self.contrast_enhancement()
         super().process_analog_signals()
         rotated_images = self.roatate_by_frame()
         masked_unregistered = self.add_circle_mask(rotated_images)

derotation/config/full_rotation.yml

@@ -1,28 +1,35 @@
 paths_read:
-  path_to_randperm: "your_path_to/stimlus_randperm.mat"
-  path_to_aux: "your_path_to/rotation.bin"
-  path_to_tif: "your_path_to/rotation.tif"
+  path_to_randperm: /Users/lauraporta/local_data/rotation/stimlus_randperm.mat
+  path_to_aux: /Users/lauraporta/local_data/rotation/230731_25_micron_grid/aux_stim/230731_grid_1_001.bin
+  path_to_tif: /Users/lauraporta/local_data/rotation/230731_25_micron_grid/imaging/rotation_zf2_all_speeds_00002_enhanced.tif
 paths_write:
-  debug_plots_folder: "your_path_to/debug_plots/"
-  logs_folder: "your_path_to/logs/"
-  derotated_tiff_folder: "your_path_to/data_folder/"
-  saving_name: "derotated_image_stack"
+  debug_plots_folder: /Users/lauraporta/local_data/rotation/230731_25_micron_grid/full/debug_plots/
+  logs_folder: /Users/lauraporta/local_data/rotation/230731_25_micron_grid/full/logs/
+  derotated_tiff_folder: /Users/lauraporta/local_data/rotation/230731_25_micron_grid/full/derotated/
+  saving_name: derotated_image_stack_CE
+# paths_read:
+#   path_to_randperm: /Users/lauraporta/local_data/rotation/stimlus_randperm.mat
+#   path_to_aux: /Users/lauraporta/local_data/rotation/230802_CAA_1120182/aux_stim/230802_CAA_1120182_rotation_1_001.bin
+#   path_to_tif: /Users/lauraporta/local_data/rotation/230802_CAA_1120182/imaging/rotation_00001.tif
+# paths_write:
+#   debug_plots_folder: /Users/lauraporta/local_data/rotation/230802_CAA_1120182/full/debug_plots/
+#   logs_folder: /Users/lauraporta/local_data/rotation/230802_CAA_1120182/full/logs/
+#   derotated_tiff_folder: /Users/lauraporta/local_data/rotation/230802_CAA_1120182/full/derotated/
+#   saving_name: derotated_image_stack_NO_ce
 
-
-channel_names: [
-    "camera",
-    "scanimage_frameclock",
-    "scanimage_lineclock",
-    "photodiode2",
-    "PI_rotON",
-    "PI_rotticks",
-]
+channel_names:
+  - camera
+  - scanimage_frameclock
+  - scanimage_lineclock
+  - photodiode2
+  - PI_rotON
+  - PI_rotticks
 
 rotation_increment: 0.2
-adjust_increment: True
+adjust_increment: false
 rot_deg: 360
 
-debugging_plots: True
+debugging_plots: false
 
 contrast_enhancement: 0.35
 
@@ -35,5 +42,5 @@ analog_signals_processing:
   angle_interpolation_artifact_threshold: 0.15
 
 interpolation:
-  line_use_start: True
-  frame_use_start: True
+  line_use_start: true
+  frame_use_start: true

derotation/config/incremental_rotation.yml

@@ -1,12 +1,12 @@
 paths_read:
-  path_to_randperm: "your_path_to/stimlus_randperm.mat"
-  path_to_aux: "your_path_to/rotation.bin"
-  path_to_tif: "your_path_to/rotation.tif"
+  path_to_randperm: "/Users/lauraporta/local_data/rotation/stimlus_randperm.mat"
+  path_to_aux: "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/aux_stim/230802_CAA_1120182_rotationincrement_1_001.bin"
+  path_to_tif: "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/imaging/rotation_increment_00001.tif"
 paths_write:
-  debug_plots_folder: "your_path_to/debug_plots/"
-  logs_folder: "your_path_to/logs/"
-  derotated_tiff_folder: "your_path_to/data_folder/"
-  saving_name: "derotated_image_stack"
+  debug_plots_folder: "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/incremental/debug_plots/"
+  logs_folder: "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/incremental/logs/"
+  derotated_tiff_folder: "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/incremental/derotated/"
+  saving_name: "derotated_incremental_image_stack_NO_ce"
 
 
 channel_names: [
@@ -22,7 +22,7 @@ rotation_increment: 0.2
 adjust_increment: True
 rot_deg: 360
 
-debugging_plots: True
+debugging_plots: False
 
 contrast_enhancement: 0.35
 

docs/source/conf.py

@@ -75,22 +75,22 @@
 # Automatically generate stub pages for API
 autosummary_generate = True
 numpydoc_class_members_toctree = False  # stops stubs warning
-#toc_object_entries_show_parents = "all"
+# toc_object_entries_show_parents = "all"
 html_show_sourcelink = False
 
-#html_sidebars = {  this is not working...
+# html_sidebars = {  this is not working...
 #  "index": [],
 #  "**": [],
-#}
+# }
 
 autodoc_default_options = {
-    'members': True,
+    "members": True,
     "member-order": "bysource",
-    'special-members': False,
-    'private-members': False,
-    'inherited-members': False,
-    'undoc-members': True,
-    'exclude-members': "",
+    "special-members": False,
+    "private-members": False,
+    "inherited-members": False,
+    "undoc-members": True,
+    "exclude-members": "",
 }
 
 # List of patterns, relative to source directory, that match files and

examples/improve_video_using_suite2p_metrics.py

@@ -6,35 +6,62 @@
 from suite2p.io import BinaryFile
 from suite2p.registration.nonrigid import make_blocks, spatial_taper
 
-from derotation.analysis.incremental_rotation_pipeline import (
-    IncrementalPipeline,
-)
-
-derotator = IncrementalPipeline("incremental_rotation")
-derotator()
+# derotator = IncrementalPipeline("incremental_rotation")
+# derotator()
 
 
-# extract luminance variations across angles
-zero_rotation_mean_image = derotator.get_target_image(derotator.masked)
-mean_images_across_angles = derotator.calculate_mean_images(derotator.masked)
+# # extract luminance variations across angles
+# zero_rotation_mean_image = derotator.get_target_image(derotator.masked)
+# mean_images_across_angles = derotator.calculate_mean_images(derotator.masked)
 
 
 #  load registered bin file of suite2p
 path_to_bin_file = Path(
     "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/incremental/derotated/suite2p/plane0/data.bin"
 )
-shape_image = zero_rotation_mean_image.shape
+shape_image = [256, 256]
 registered = BinaryFile(
     Ly=shape_image[0], Lx=shape_image[0], filename=path_to_bin_file
+).file
+
+time, x, y = registered.shape
+registered = registered.reshape(time, x * y)
+model = PCA(n_components=10, random_state=0).fit(registered)
+
+
+print("debug")
+
+
+path_options = Path("/Users/lauraporta/local_data/laura_ops.npy")
+ops = np.load(path_options, allow_pickle=True).item()
+
+bin_size = int(
+    max(1, ops["nframes"] // ops["nbinned"], np.round(ops["tau"] * ops["fs"]))
 )
-plt.imshow(registered[0])
-plt.show()
 
-# load options
+with BinaryFile(filename=path_to_bin_file, Ly=ops["Ly"], Lx=ops["Lx"]) as f:
+    registered = f.bin_movie(
+        bin_size=bin_size,
+        bad_frames=ops.get("badframes"),
+        y_range=ops["yrange"],
+        x_range=ops["xrange"],
+    )
+
+mov_mean = registered.mean(axis=0)
+registered -= mov_mean
+model = PCA(n_components=8, random_state=0).fit(registered)
+
+result = (registered @ model.components_.T) @ model.components_
+
+
+# use PCA as in the suite2p code - this takes in account for non rigid
+# registration, that we are not going to do
 path_options = Path("/Users/lauraporta/local_data/laura_ops.npy")
-ops = np.load(path_options)
+ops = np.load(path_options, allow_pickle=True).item()
+
+mov_mean = registered.mean(axis=0)
+registered -= mov_mean
 
-# use PCA as in the suite2p code
 block_size = [ops["block_size"][0] // 2, ops["block_size"][1] // 2]
 nframes, Ly, Lx = registered.shape
 yblock, xblock, _, block_size, _ = make_blocks(Ly, Lx, block_size=block_size)
@@ -54,5 +81,19 @@
     block_re[i] = (block @ model.components_.T) @ model.components_
     norm[yblock[i][0] : yblock[i][-1], xblock[i][0] : xblock[i][-1]] += maskMul
 
+reconstruction = np.zeros_like(registered)
+
+block_re = block_re.reshape(nblocks, nframes, Lyb, Lxb)
+block_re *= maskMul
+for i in range(nblocks):
+    reconstruction[
+        :, yblock[i][0] : yblock[i][-1], xblock[i][0] : xblock[i][-1]
+    ] += block_re[i]
+reconstruction /= norm
+reconstruction += mov_mean
+
+plt.imshow(norm)
+plt.show()
+
 
 print("debug")