shinestacker 1.2.1__py3-none-any.whl → 1.3.1__py3-none-any.whl

shinestacker/_version.py

@@ -1 +1 @@
-__version__ = '1.2.1'
+__version__ = '1.3.1'

shinestacker/algorithms/align.py

@@ -1,14 +1,17 @@
 # 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
+import matplotlib.pyplot as plt
+import matplotlib
 from .. config.constants import constants
 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
+matplotlib.use('Agg')
 
 _DEFAULT_FEATURE_CONFIG = {
     'detector': constants.DEFAULT_DETECTOR,
@@ -20,7 +23,7 @@ _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 = {
@@ -74,7 +77,7 @@ def decompose_affine_matrix(m):
 
 def check_affine_matrix(m, img_shape, affine_thresholds=_AFFINE_THRESHOLDS):
     if affine_thresholds is None:
-        return True, "No thresholds provided"
+        return True, "No thresholds provided", None
     (scale_x, scale_y), rotation, shear, (tx, ty) = decompose_affine_matrix(m)
     h, w = img_shape[:2]
     reasons = []
@@ -93,13 +96,14 @@ def check_affine_matrix(m, img_shape, affine_thresholds=_AFFINE_THRESHOLDS):
     if abs(ty) > max_ty:
         reasons.append(f"y-translation too large (|{ty:.1f}| > {max_ty:.1f})")
     if reasons:
-        return False, "; ".join(reasons)
-    return True, "Transformation within acceptable limits"
+        return False, "; ".join(reasons), None
+    return True, "Transformation within acceptable limits", \
+        (scale_x, scale_y, tx, ty, rotation, shear)
 
 
 def check_homography_distortion(m, img_shape, homography_thresholds=_HOMOGRAPHY_THRESHOLDS):
     if homography_thresholds is None:
-        return True, "No thresholds provided"
+        return True, "No thresholds provided", None
     h, w = img_shape[:2]
     corners = np.array([[0, 0], [w, 0], [w, h], [0, h]], dtype=np.float32)
     transformed = cv2.perspectiveTransform(corners.reshape(1, -1, 2), m).reshape(-1, 2)
@@ -126,8 +130,20 @@ def check_homography_distortion(m, img_shape, homography_thresholds=_HOMOGRAPHY_
     if max_angle_dev > homography_thresholds['max_skew']:
         reasons.append(f"angle distortion too large ({max_angle_dev:.1f}°)")
     if reasons:
-        return False, "; ".join(reasons)
-    return True, "Transformation within acceptable limits"
+        return False, "; ".join(reasons), None
+    return True, "Transformation within acceptable limits", \
+        (area_ratio, aspect_ratio, max_angle_dev)
+
+
+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}', None
 
 
 def get_good_matches(des_0, des_ref, matching_config=None):
@@ -172,7 +188,23 @@ def validate_align_config(detector, descriptor, match_method):
                          " require matching method Hamming distance")
 
 
-def detect_and_compute(img_0, img_ref, 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']
@@ -180,19 +212,6 @@ def detect_and_compute(img_0, img_ref, feature_config=None, matching_config=None
     match_method = matching_config['match_method']
     validate_align_config(feature_config_detector, feature_config_descriptor, match_method)
     img_bw_0, img_bw_ref = img_bw_8bit(img_0), img_bw_8bit(img_ref)
-    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
-    }
     detector = detector_map[feature_config_detector]()
     if feature_config_detector == feature_config_descriptor and \
        feature_config_detector in (constants.DETECTOR_SIFT,
@@ -236,6 +255,37 @@ def find_transform(src_pts, dst_pts, transform=constants.DEFAULT_TRANSFORM,
     return result
 
 
+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 plot_matches(msk, img_ref_sub, img_0_sub, kp_ref, kp_0, good_matches, plot_path):
+    matches_mask = msk.ravel().tolist()
+    img_match = cv2.cvtColor(cv2.drawMatches(
+        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=constants.PLT_FIG_SIZE)
+    plt.imshow(img_match, 'gray')
+    save_plot(plot_path)
+
+
 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,
@@ -265,8 +315,8 @@ def align_images(img_ref, img_0, feature_config=None, matching_config=None, alig
             img_ref_sub = img_subsample(img_ref, subsample, fast_subsampling)
         else:
             img_0_sub, img_ref_sub = img_0, img_ref
-        kp_0, kp_ref, good_matches = detect_and_compute(img_0_sub, img_ref_sub,
-                                                        feature_config, matching_config)
+        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
@@ -281,54 +331,32 @@ def align_images(img_ref, img_0, feature_config=None, matching_config=None, alig
     m = None
     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_ref[m.trainIdx].pt for m in good_matches]).reshape(-1, 1, 2)
+        src_pts = np.float32(
+            [kp_0[match.queryIdx].pt for match in good_matches]).reshape(-1, 1, 2)
+        dst_pts = np.float32(
+            [kp_ref[match.trainIdx].pt for match 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',
                                             'align_confidence', 'refine_iters']))
         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_ref_sub),
-                kp_ref, good_matches, None, matchColor=(0, 255, 0),
-                singlePointColor=None, matchesMask=matches_mask,
-                flags=2), cv2.COLOR_BGR2RGB)
-            plt.figure(figsize=constants.PLT_FIG_SIZE)
-            plt.imshow(img_match, 'gray')
-            save_plot(plot_path)
+            plot_matches(msk, img_ref_sub, img_0_sub, kp_ref, kp_0, good_matches, 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, _result = 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']()
@@ -357,12 +385,12 @@ def align_images(img_ref, img_0, feature_config=None, matching_config=None, alig
     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 {})}
@@ -380,69 +408,36 @@ 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 align_images(self, idx, img_ref, img_0):
-        idx_str = f"{idx:04d}"
-        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(
-                f': {msg}', constants.LOG_COLOR_WARNING),
-            'save_plot': lambda plot_path: self.process.callback(
-                'save_plot', self.process.id,
-                f"{self.process.name}: matches\nframe {idx_str}", plot_path)
-        }
-        if self.plot_matches:
-            plot_path = f"{self.process.working_path}/{self.process.plot_path}/" \
-                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
-        n_good_matches, _m, img = align_images(
-            img_ref, img_0,
-            feature_config=self.feature_config,
-            matching_config=self.matching_config,
-            alignment_config=self.alignment_config,
-            plot_path=plot_path,
-            callbacks=callbacks,
-            affine_thresholds=affine_thresholds,
-            homography_thresholds=homography_thresholds
-        )
-        self.n_matches[idx] = n_good_matches
-        if n_good_matches < self.min_matches:
-            self.process.sub_message(color_str(f": image not aligned, too few matches found: "
-                                     f"{n_good_matches}", constants.LOG_COLOR_WARNING),
-                                     level=logging.WARNING)
-            return None
-        return img
+    def get_transform_thresholds(self):
+        return _AFFINE_THRESHOLDS, _HOMOGRAPHY_THRESHOLDS
 
-    def begin(self, process):
-        self.process = process
-        self.n_matches = np.zeros(process.total_action_counts)
+    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_matches) + 1, dtype=int)
+            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_matches[no_ref]
+            y = np.array(self._n_good_matches)[no_ref]
             if self.process.ref_idx == 0:
                 y_max = y[1]
             elif self.process.ref_idx >= len(y):
@@ -464,5 +459,50 @@ class AlignFrames(SubAction):
                         f"{self.process.name}-matches.pdf"
             save_plot(plot_path)
             plt.close('all')
-            self.process.callback('save_plot', self.process.id,
+            self.process.callback(constants.CALLBACK_SAVE_PLOT, self.process.id,
                                   f"{self.process.name}: matches", plot_path)
+
+
+class AlignFrames(AlignFramesBase):
+    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.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(
+                constants.CALLBACK_SAVE_PLOT, self.process.id,
+                f"{self.process.name}: matches\nframe {idx_str}", plot_path)
+        }
+        if self.plot_matches:
+            plot_path = os.path.join(
+                self.process.working_path,
+                self.process.plot_path,
+                f"{self.process.name}-matches-{idx_str}.pdf")
+        else:
+            plot_path = None
+        affine_thresholds, homography_thresholds = self.get_transform_thresholds()
+        n_good_matches, _m, img = align_images(
+            img_ref, img_0,
+            feature_config=self.feature_config,
+            matching_config=self.matching_config,
+            alignment_config=self.alignment_config,
+            plot_path=plot_path,
+            callbacks=callbacks,
+            affine_thresholds=affine_thresholds,
+            homography_thresholds=homography_thresholds
+        )
+        self._n_good_matches[idx] = n_good_matches
+        if 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 sequential_processing(self):
+        return True

shinestacker/algorithms/align_auto.py

@@ -0,0 +1,76 @@
+# pylint: disable=C0114, C0115, C0116, W0718, R0912, R0915, E1101, R0914, R0911, E0606, R0801, R0902
+import os
+import numpy as np
+from ..config.constants import constants
+from .align import AlignFramesBase, AlignFrames
+from .align_parallel import AlignFramesParallel
+from .utils import get_first_image_file, get_img_metadata, read_img
+
+
+class AlignFramesAuto(AlignFramesBase):
+    def __init__(self, enabled=True, feature_config=None, matching_config=None,
+                 alignment_config=None, **kwargs):
+        self.mode = kwargs.pop('mode', constants.DEFAULT_ALIGN_MODE)
+        self.memory_limit = kwargs.pop('memory_limit', constants.DEFAULT_ALIGN_MEMORY_LIMIT_GB)
+        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
+        super().__init__(enabled=True, feature_config=None, matching_config=None,
+                         alignment_config=None, **kwargs)
+        available_cores = os.cpu_count() or 1
+        self.num_threads = min(self.max_threads, available_cores)
+        self._implementation = None
+        self.overhead = 30.0
+
+    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):
+                    shape, dtype = get_img_metadata(
+                        read_img(get_first_image_file(process.input_filepaths())))
+                    bytes_per_pixel = 3 * np.dtype(dtype).itemsize
+                    img_memory = bytes_per_pixel * float(shape[0]) * float(shape[1]) * \
+                        self.overhead / constants.ONE_GIGA
+                    num_threads = max(
+                        1,
+                        int(round(self.memory_limit) / img_memory))
+                    num_threads = min(num_threads, 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()