shinestacker 1.2.0__py3-none-any.whl → 1.3.0__py3-none-any.whl

shinestacker/_version.py

@@ -1 +1 @@
-__version__ = '1.2.0'
+__version__ = '1.3.0'

shinestacker/algorithms/align.py

@@ -1,11 +1,12 @@
 # pylint: disable=C0114, C0115, C0116, E1101, R0914, R0913, R0917, R0912, R0915, R0902, E1121, W0102
-import logging
+import os
 import math
+import logging
 import numpy as np
 import matplotlib.pyplot as plt
 import cv2
 from .. config.constants import constants
-from .. core.exceptions import AlignmentError, InvalidOptionError
+from .. core.exceptions import InvalidOptionError
 from .. core.colors import color_str
 from .utils import img_8bit, img_bw_8bit, save_plot, img_subsample
 from .stack_framework import SubAction
@@ -20,7 +21,7 @@ _DEFAULT_MATCHING_CONFIG = {
     'flann_idx_kdtree': constants.DEFAULT_FLANN_IDX_KDTREE,
     'flann_trees': constants.DEFAULT_FLANN_TREES,
     'flann_checks': constants.DEFAULT_FLANN_CHECKS,
-    'threshold': constants.DEFAULT_ALIGN_THRESHOLD
+    'threshold': constants.DEFAULT_ALIGN_THRESHOLD,
 }
 
 _DEFAULT_ALIGNMENT_CONFIG = {
@@ -130,7 +131,18 @@ def check_homography_distortion(m, img_shape, homography_thresholds=_HOMOGRAPHY_
     return True, "Transformation within acceptable limits"
 
 
-def get_good_matches(des_0, des_1, matching_config=None):
+def check_transform(m, img_0, transform_type,
+                    affine_thresholds, homography_thresholds):
+    if transform_type == constants.ALIGN_RIGID:
+        return check_affine_matrix(
+            m, img_0.shape, affine_thresholds)
+    if transform_type == constants.ALIGN_HOMOGRAPHY:
+        return check_homography_distortion(
+            m, img_0.shape, homography_thresholds)
+    return False, f'invalid transfrom option {transform_type}'
+
+
+def get_good_matches(des_0, des_ref, matching_config=None):
     matching_config = {**_DEFAULT_MATCHING_CONFIG, **(matching_config or {})}
     match_method = matching_config['match_method']
     good_matches = []
@@ -139,12 +151,12 @@ def get_good_matches(des_0, des_1, matching_config=None):
             {'algorithm': matching_config['flann_idx_kdtree'],
              'trees': matching_config['flann_trees']},
             {'checks': matching_config['flann_checks']})
-        matches = flann.knnMatch(des_0, des_1, k=2)
+        matches = flann.knnMatch(des_0, des_ref, k=2)
         good_matches = [m for m, n in matches
                         if m.distance < matching_config['threshold'] * n.distance]
     elif match_method == constants.MATCHING_NORM_HAMMING:
         bf = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)
-        good_matches = sorted(bf.match(des_0, des_1), key=lambda x: x.distance)
+        good_matches = sorted(bf.match(des_0, des_ref), key=lambda x: x.distance)
     else:
         raise InvalidOptionError(
             'match_method', match_method,
@@ -172,39 +184,42 @@ def validate_align_config(detector, descriptor, match_method):
                          " require matching method Hamming distance")
 
 
-def detect_and_compute(img_0, img_1, feature_config=None, matching_config=None):
+detector_map = {
+    constants.DETECTOR_SIFT: cv2.SIFT_create,
+    constants.DETECTOR_ORB: cv2.ORB_create,
+    constants.DETECTOR_SURF: cv2.FastFeatureDetector_create,
+    constants.DETECTOR_AKAZE: cv2.AKAZE_create,
+    constants.DETECTOR_BRISK: cv2.BRISK_create
+}
+
+descriptor_map = {
+    constants.DESCRIPTOR_SIFT: cv2.SIFT_create,
+    constants.DESCRIPTOR_ORB: cv2.ORB_create,
+    constants.DESCRIPTOR_AKAZE: cv2.AKAZE_create,
+    constants.DETECTOR_BRISK: cv2.BRISK_create
+}
+
+
+def detect_and_compute_matches(img_ref, img_0, feature_config=None, matching_config=None):
     feature_config = {**_DEFAULT_FEATURE_CONFIG, **(feature_config or {})}
     matching_config = {**_DEFAULT_MATCHING_CONFIG, **(matching_config or {})}
     feature_config_detector = feature_config['detector']
     feature_config_descriptor = feature_config['descriptor']
     match_method = matching_config['match_method']
     validate_align_config(feature_config_detector, feature_config_descriptor, match_method)
-    img_bw_0, img_bw_1 = img_bw_8bit(img_0), img_bw_8bit(img_1)
-    detector_map = {
-        constants.DETECTOR_SIFT: cv2.SIFT_create,
-        constants.DETECTOR_ORB: cv2.ORB_create,
-        constants.DETECTOR_SURF: cv2.FastFeatureDetector_create,
-        constants.DETECTOR_AKAZE: cv2.AKAZE_create,
-        constants.DETECTOR_BRISK: cv2.BRISK_create
-    }
-    descriptor_map = {
-        constants.DESCRIPTOR_SIFT: cv2.SIFT_create,
-        constants.DESCRIPTOR_ORB: cv2.ORB_create,
-        constants.DESCRIPTOR_AKAZE: cv2.AKAZE_create,
-        constants.DETECTOR_BRISK: cv2.BRISK_create
-    }
+    img_bw_0, img_bw_ref = img_bw_8bit(img_0), img_bw_8bit(img_ref)
     detector = detector_map[feature_config_detector]()
     if feature_config_detector == feature_config_descriptor and \
        feature_config_detector in (constants.DETECTOR_SIFT,
                                    constants.DETECTOR_AKAZE,
                                    constants.DETECTOR_BRISK):
         kp_0, des_0 = detector.detectAndCompute(img_bw_0, None)
-        kp_1, des_1 = detector.detectAndCompute(img_bw_1, None)
+        kp_ref, des_ref = detector.detectAndCompute(img_bw_ref, None)
     else:
         descriptor = descriptor_map[feature_config_descriptor]()
         kp_0, des_0 = descriptor.compute(img_bw_0, detector.detect(img_bw_0, None))
-        kp_1, des_1 = descriptor.compute(img_bw_1, detector.detect(img_bw_1, None))
-    return kp_0, kp_1, get_good_matches(des_0, des_1, matching_config)
+        kp_ref, des_ref = descriptor.compute(img_bw_ref, detector.detect(img_bw_ref, None))
+    return kp_0, kp_ref, get_good_matches(des_0, des_ref, matching_config)
 
 
 def find_transform(src_pts, dst_pts, transform=constants.DEFAULT_TRANSFORM,
@@ -236,7 +251,26 @@ def find_transform(src_pts, dst_pts, transform=constants.DEFAULT_TRANSFORM,
     return result
 
 
-def align_images(img_1, img_0, feature_config=None, matching_config=None, alignment_config=None,
+def rescale_trasnsform(m, w0, h0, w_sub, h_sub, subsample, transform):
+    if transform == constants.ALIGN_HOMOGRAPHY:
+        low_size = np.float32([[0, 0], [0, h_sub], [w_sub, h_sub], [w_sub, 0]])
+        high_size = np.float32([[0, 0], [0, h0], [w0, h0], [w0, 0]])
+        scale_up = cv2.getPerspectiveTransform(low_size, high_size)
+        scale_down = cv2.getPerspectiveTransform(high_size, low_size)
+        m = scale_up @ m @ scale_down
+    elif transform == constants.ALIGN_RIGID:
+        rotation = m[:2, :2]
+        translation = m[:, 2]
+        translation_fullres = translation * subsample
+        m = np.empty((2, 3), dtype=np.float32)
+        m[:2, :2] = rotation
+        m[:, 2] = translation_fullres
+    else:
+        return 0
+    return m
+
+
+def align_images(img_ref, img_0, feature_config=None, matching_config=None, alignment_config=None,
                  plot_path=None, callbacks=None,
                  affine_thresholds=_AFFINE_THRESHOLDS,
                  homography_thresholds=_HOMOGRAPHY_THRESHOLDS):
@@ -250,11 +284,11 @@ def align_images(img_1, img_0, feature_config=None, matching_config=None, alignm
     min_matches = 4 if alignment_config['transform'] == constants.ALIGN_HOMOGRAPHY else 3
     if callbacks and 'message' in callbacks:
         callbacks['message']()
-    h_ref, w_ref = img_1.shape[:2]
+    h_ref, w_ref = img_ref.shape[:2]
     h0, w0 = img_0.shape[:2]
     subsample = alignment_config['subsample']
     if subsample == 0:
-        img_res = (float(h0) / 1000) * (float(w0) / 1000)
+        img_res = (float(h0) / constants.ONE_KILO) * (float(w0) / constants.ONE_KILO)
         target_res = constants.DEFAULT_ALIGN_RES_TARGET_MPX
         subsample = int(1 + math.floor(img_res / target_res))
     fast_subsampling = alignment_config['fast_subsampling']
@@ -262,11 +296,11 @@ def align_images(img_1, img_0, feature_config=None, matching_config=None, alignm
     while True:
         if subsample > 1:
             img_0_sub = img_subsample(img_0, subsample, fast_subsampling)
-            img_1_sub = img_subsample(img_1, subsample, fast_subsampling)
+            img_ref_sub = img_subsample(img_ref, subsample, fast_subsampling)
         else:
-            img_0_sub, img_1_sub = img_0, img_1
-        kp_0, kp_1, good_matches = detect_and_compute(img_0_sub, img_1_sub,
-                                                      feature_config, matching_config)
+            img_0_sub, img_ref_sub = img_0, img_ref
+        kp_0, kp_ref, good_matches = detect_and_compute_matches(
+            img_ref_sub, img_0_sub, feature_config, matching_config)
         n_good_matches = len(good_matches)
         if n_good_matches > min_good_matches or subsample == 1:
             break
@@ -282,7 +316,7 @@ def align_images(img_1, img_0, feature_config=None, matching_config=None, alignm
     if n_good_matches >= min_matches:
         transform = alignment_config['transform']
         src_pts = np.float32([kp_0[m.queryIdx].pt for m in good_matches]).reshape(-1, 1, 2)
-        dst_pts = np.float32([kp_1[m.trainIdx].pt for m in good_matches]).reshape(-1, 1, 2)
+        dst_pts = np.float32([kp_ref[m.trainIdx].pt for m in good_matches]).reshape(-1, 1, 2)
         m, msk = find_transform(src_pts, dst_pts, transform, alignment_config['align_method'],
                                 *(alignment_config[k]
                                   for k in ['rans_threshold', 'max_iters',
@@ -290,47 +324,30 @@ def align_images(img_1, img_0, feature_config=None, matching_config=None, alignm
         if plot_path is not None:
             matches_mask = msk.ravel().tolist()
             img_match = cv2.cvtColor(cv2.drawMatches(
-                img_8bit(img_0_sub), kp_0, img_8bit(img_1_sub),
-                kp_1, good_matches, None, matchColor=(0, 255, 0),
+                img_8bit(img_0_sub), kp_0, img_8bit(img_ref_sub),
+                kp_ref, good_matches, None, matchColor=(0, 255, 0),
                 singlePointColor=None, matchesMask=matches_mask,
                 flags=2), cv2.COLOR_BGR2RGB)
-            plt.figure(figsize=(10, 5))
+            plt.figure(figsize=constants.PLT_FIG_SIZE)
             plt.imshow(img_match, 'gray')
             save_plot(plot_path)
             if callbacks and 'save_plot' in callbacks:
                 callbacks['save_plot'](plot_path)
         h_sub, w_sub = img_0_sub.shape[:2]
         if subsample > 1:
-            if transform == constants.ALIGN_HOMOGRAPHY:
-                low_size = np.float32([[0, 0], [0, h_sub], [w_sub, h_sub], [w_sub, 0]])
-                high_size = np.float32([[0, 0], [0, h0], [w0, h0], [w0, 0]])
-                scale_up = cv2.getPerspectiveTransform(low_size, high_size)
-                scale_down = cv2.getPerspectiveTransform(high_size, low_size)
-                m = scale_up @ m @ scale_down
-            elif transform == constants.ALIGN_RIGID:
-                rotation = m[:2, :2]
-                translation = m[:, 2]
-                translation_fullres = translation * subsample
-                m = np.empty((2, 3), dtype=np.float32)
-                m[:2, :2] = rotation
-                m[:, 2] = translation_fullres
-            else:
+            m = rescale_trasnsform(m, w0, h0, w_sub, h_sub, subsample, transform)
+            if m is None:
                 raise InvalidOptionError("transform", transform)
-
         transform_type = alignment_config['transform']
-        is_valid = True
-        reason = ""
-        if transform_type == constants.ALIGN_RIGID:
-            is_valid, reason = check_affine_matrix(
-                m, img_0.shape, affine_thresholds)
-        elif transform_type == constants.ALIGN_HOMOGRAPHY:
-            is_valid, reason = check_homography_distortion(
-                m, img_0.shape, homography_thresholds)
+        is_valid, reason = check_transform(
+            m, img_0, transform_type,
+            affine_thresholds, homography_thresholds)
         if not is_valid:
             if callbacks and 'warning' in callbacks:
                 callbacks['warning'](f"invalid transformation: {reason}")
+            if alignment_config['abort_abnormal']:
+                raise RuntimeError("invalid transformation: {reason}")
             return n_good_matches, None, None
-
         if callbacks and 'align_message' in callbacks:
             callbacks['align_message']()
         img_mask = np.ones_like(img_0, dtype=np.uint8)
@@ -358,12 +375,12 @@ def align_images(img_1, img_0, feature_config=None, matching_config=None, alignm
     return n_good_matches, m, img_warp
 
 
-class AlignFrames(SubAction):
+class AlignFramesBase(SubAction):
     def __init__(self, enabled=True, feature_config=None, matching_config=None,
                  alignment_config=None, **kwargs):
         super().__init__(enabled)
         self.process = None
-        self.n_matches = None
+        self._n_good_matches = None
         self.feature_config = {**_DEFAULT_FEATURE_CONFIG, **(feature_config or {})}
         self.matching_config = {**_DEFAULT_MATCHING_CONFIG, **(matching_config or {})}
         self.alignment_config = {**_DEFAULT_ALIGNMENT_CONFIG, **(alignment_config or {})}
@@ -381,27 +398,78 @@ class AlignFrames(SubAction):
             if k in kwargs:
                 self.alignment_config[k] = kwargs[k]
 
+    def align_images(self, idx, img_ref, img_0):
+        pass
+
+    def print_message(self, msg, color=constants.LOG_COLOR_LEVEL_3, level=logging.INFO):
+        self.process.print_message(color_str(msg, color), level=level)
+
+    def begin(self, process):
+        self.process = process
+        self._n_good_matches = np.zeros(process.total_action_counts)
+
     def run_frame(self, idx, ref_idx, img_0):
         if idx == self.process.ref_idx:
             return img_0
         img_ref = self.process.img_ref(ref_idx)
         return self.align_images(idx, img_ref, img_0)
 
-    def sub_msg(self, msg, color=constants.LOG_COLOR_LEVEL_3):
-        self.process.sub_message_r(color_str(msg, color))
+    def get_transform_thresholds(self):
+        return _AFFINE_THRESHOLDS, _HOMOGRAPHY_THRESHOLDS
+
+    def image_str(self, idx):
+        return f"image: {self.process.idx_tot_str(idx)}, " \
+               f"{os.path.basename(self.process.input_filepath(idx))}"
+
+    def end(self):
+        if self.plot_summary:
+            plt.figure(figsize=constants.PLT_FIG_SIZE)
+            x = np.arange(1, len(self._n_good_matches) + 1, dtype=int)
+            no_ref = x != self.process.ref_idx + 1
+            x = x[no_ref]
+            y = self._n_good_matches[no_ref]
+            if self.process.ref_idx == 0:
+                y_max = y[1]
+            elif self.process.ref_idx >= len(y):
+                y_max = y[-1]
+            else:
+                y_max = (y[self.process.ref_idx - 1] + y[self.process.ref_idx]) / 2
+
+            plt.plot([self.process.ref_idx + 1, self.process.ref_idx + 1],
+                     [0, y_max], color='cornflowerblue', linestyle='--', label='reference frame')
+            plt.plot([x[0], x[-1]], [self.min_matches, self.min_matches], color='lightgray',
+                     linestyle='--', label='min. matches')
+            plt.plot(x, y, color='navy', label='matches')
+            plt.xlabel('frame')
+            plt.ylabel('# of matches')
+            plt.legend()
+            plt.ylim(0)
+            plt.xlim(x[0], x[-1])
+            plot_path = f"{self.process.working_path}/{self.process.plot_path}/" \
+                        f"{self.process.name}-matches.pdf"
+            save_plot(plot_path)
+            plt.close('all')
+            self.process.callback(constants.CALLBACK_SAVE_PLOT, self.process.id,
+                                  f"{self.process.name}: matches", plot_path)
+
 
-    def align_images(self, idx, img_1, img_0):
+class AlignFrames(AlignFramesBase):
+    def __init__(self, enabled=True, feature_config=None, matching_config=None,
+                 alignment_config=None, **kwargs):
+        super().__init__(enabled)
+
+    def align_images(self, idx, img_ref, img_0):
         idx_str = f"{idx:04d}"
+        idx_tot_str = self.process.idx_tot_str(idx)
         callbacks = {
-            'message': lambda: self.sub_msg(': find matches'),
-            'matches_message': lambda n: self.sub_msg(f": good matches: {n}"),
-            'align_message': lambda: self.sub_msg(': align images'),
-            'ecc_message': lambda: self.sub_msg(": ecc refinement"),
-            'blur_message': lambda: self.sub_msg(': blur borders'),
-            'warning': lambda msg: self.sub_msg(
+            'message': lambda: self.print_message(f'{idx_tot_str}: find matches'),
+            'matches_message': lambda n: self.print_message(f'{idx_tot_str}: good matches: {n}'),
+            'align_message': lambda: self.print_message(f'{idx_tot_str}: align images'),
+            'blur_message': lambda: self.print_message(f'{idx_tot_str}: blur borders'),
+            'warning': lambda msg: self.print_message(
                 f': {msg}', constants.LOG_COLOR_WARNING),
             'save_plot': lambda plot_path: self.process.callback(
-                'save_plot', self.process.id,
+                constants.CALLBACK_SAVE_PLOT, self.process.id,
                 f"{self.process.name}: matches\nframe {idx_str}", plot_path)
         }
         if self.plot_matches:
@@ -409,14 +477,9 @@ class AlignFrames(SubAction):
                 f"{self.process.name}-matches-{idx_str}.pdf"
         else:
             plot_path = None
-        if self.alignment_config['abort_abnormal']:
-            affine_thresholds = _AFFINE_THRESHOLDS
-            homography_thresholds = _HOMOGRAPHY_THRESHOLDS
-        else:
-            affine_thresholds = None
-            homography_thresholds = None
+        affine_thresholds, homography_thresholds = self.get_transform_thresholds()
         n_good_matches, _m, img = align_images(
-            img_1, img_0,
+            img_ref, img_0,
             feature_config=self.feature_config,
             matching_config=self.matching_config,
             alignment_config=self.alignment_config,
@@ -425,43 +488,13 @@ class AlignFrames(SubAction):
             affine_thresholds=affine_thresholds,
             homography_thresholds=homography_thresholds
         )
-        self.n_matches[idx] = n_good_matches
+        self._n_good_matches[idx] = n_good_matches
         if n_good_matches < self.min_matches:
-            self.process.sub_message(f": image not aligned, too few matches found: "
-                                     f"{n_good_matches}", level=logging.CRITICAL)
-            raise AlignmentError(idx, f"Image not aligned, too few matches found: "
-                                 f"{n_good_matches} < {self.min_matches}")
+            self.process.print_message(
+                f"{self.image_str(idx)} not aligned, too few matches found: "
+                f"{n_good_matches}")
+            return None
         return img
 
-    def begin(self, process):
-        self.process = process
-        self.n_matches = np.zeros(process.counts)
-
-    def end(self):
-        if self.plot_summary:
-            plt.figure(figsize=(10, 5))
-            x = np.arange(1, len(self.n_matches) + 1, dtype=int)
-            no_ref = x != self.process.ref_idx + 1
-            x = x[no_ref]
-            y = self.n_matches[no_ref]
-            y_max = y[1] \
-                if self.process.ref_idx == 0 \
-                else y[-1] if self.process.ref_idx == len(y) - 1 \
-                else (y[self.process.ref_idx - 1] + y[self.process.ref_idx]) / 2
-
-            plt.plot([self.process.ref_idx + 1, self.process.ref_idx + 1],
-                     [0, y_max], color='cornflowerblue', linestyle='--', label='reference frame')
-            plt.plot([x[0], x[-1]], [self.min_matches, self.min_matches], color='lightgray',
-                     linestyle='--', label='min. matches')
-            plt.plot(x, y, color='navy', label='matches')
-            plt.xlabel('frame')
-            plt.ylabel('# of matches')
-            plt.legend()
-            plt.ylim(0)
-            plt.xlim(x[0], x[-1])
-            plot_path = f"{self.process.working_path}/{self.process.plot_path}/" \
-                        f"{self.process.name}-matches.pdf"
-            save_plot(plot_path)
-            plt.close('all')
-            self.process.callback('save_plot', self.process.id,
-                                  f"{self.process.name}: matches", plot_path)
+    def sequential_processing(self):
+        return True

shinestacker/algorithms/align_auto.py

@@ -0,0 +1,64 @@
+# pylint: disable=C0114, C0115, C0116, W0718, R0912, R0915, E1101, R0914, R0911, E0606, R0801, R0902
+import os
+from ..config.constants import constants
+from .align import AlignFramesBase, AlignFrames
+from .align_parallel import AlignFramesParallel
+
+
+class AlignFramesAuto(AlignFramesBase):
+    def __init__(self, enabled=True, feature_config=None, matching_config=None,
+                 alignment_config=None, **kwargs):
+        super().__init__(enabled=True, feature_config=None, matching_config=None,
+                         alignment_config=None, **kwargs)
+        self.mode = kwargs.pop('mode', constants.DEFAULT_ALIGN_MODE)
+        self.max_threads = kwargs.pop('max_threads', constants.DEFAULT_ALIGN_MAX_THREADS)
+        self.chunk_submit = kwargs.pop('chunk_submit', constants.DEFAULT_ALIGN_CHUNK_SUBMIT)
+        self.bw_matching = kwargs.pop('bw_matching', constants.DEFAULT_ALIGN_BW_MATCHING)
+        self.kwargs = kwargs
+        available_cores = os.cpu_count() or 1
+        self.num_threads = min(self.max_threads, available_cores)
+        self._implementation = None
+
+    def begin(self, process):
+        if self.mode == 'sequential' or self.num_threads == 1:
+            self._implementation = AlignFrames(
+                self.enabled, self.feature_config, self.matching_config, self.alignment_config,
+                **self.kwargs)
+        else:
+            if self.mode == 'parallel':
+                num_threads = self.num_threads
+                chunk_submit = self.chunk_submit
+            else:
+                if self.feature_config is not None:
+                    detector = self.feature_config.get(
+                        'detector', constants.DEFAULT_DETECTOR)
+                    descriptor = self.feature_config.get(
+                        'descriptor', constants.DEFAULT_DESCRIPTOR)
+                else:
+                    detector = constants.DEFAULT_DETECTOR
+                    descriptor = constants.DEFAULT_DESCRIPTOR
+                if detector in (constants.DETECTOR_SIFT, constants.DETECTOR_AKAZE) or \
+                        descriptor in (constants.DESCRIPTOR_SIFT, constants.DESCRIPTOR_AKAZE):
+                    num_threads = min(3, self.num_threads)
+                    chunk_submit = True
+                else:
+                    num_threads = self.num_threads
+                    chunk_submit = self.chunk_submit
+            self._implementation = AlignFramesParallel(
+                self.enabled, self.feature_config, self.matching_config, self.alignment_config,
+                max_threads=num_threads, chunk_submit=chunk_submit,
+                bw_matching=self.bw_matching,
+                **self.kwargs)
+        self._implementation.begin(process)
+
+    def align_images(self, idx, img_ref, img_0):
+        return self._implementation.align_images(idx, img_ref, img_0)
+
+    def run_frame(self, idx, ref_idx, img_0):
+        return self._implementation.run_frame(idx, ref_idx, img_0)
+
+    def sequential_processing(self):
+        return self._implementation.sequential_processing()
+
+    def end(self):
+        self._implementation.end()