def workflow(input_name,
input_type='video',
roi=None,
automatic_ap_creation=True):
"""
Execute the whole stacking workflow for a test case. This can either use a video file (.avi .mov .mp4 .ser)
or still images stored in a single directory.
:param input_name: Video file (.avi .mov .mp4 .ser) or name of a directory containing still images
:param input_type: Either "video" or "image" (see "input_name")
:param roi: If specified, tuple (y_low, y_high, x_low, x_high) with pixel bounds for "region
of interest"
:return: average, [average_roi,] color_image_with_aps, stacked_image
with: - average: global mean frame
- average_roi: mean frame restricted to ROI (only if roi is specified)
- color_image_with_aps: mean frame overlaid with alignment points and their
boxes (white) and patches (green)
"""
# Initalize the timer object used to measure execution times of program sections.
my_timer = timer()
# Images can either be extracted from a video file or a batch of single photographs. Select
# the example for the test run.
# For video file input, the Frames constructor expects the video file name for "names".
if input_type == 'video':
names = input_name
# For single image input, the Frames constructor expects a list of image file names for "names".
else:
names = [
os.path.join(input_name, name) for name in os.listdir(input_name)
]
stacked_image_name = input_name + '.stacked.tiff'
# The name of the alignment point visualization file is derived from the input video name or
# the input directory name.
ap_image_name = input_name + ".aps.tiff"
print(
"\n" +
"*************************************************************************************\n"
+ "Start processing " + str(input_name) +
"\n*************************************************************************************"
)
my_timer.create('Execution over all')
# Get configuration parameters.
configuration = Configuration()
configuration.initialize_configuration()
# Read the frames.
print("+++ Start reading frames")
my_timer.create('Read all frames')
try:
frames = Frames(configuration, names, type=input_type)
print("Number of images read: " + str(frames.number))
print("Image shape: " + str(frames.shape))
except Error as e:
print("Error: " + str(e))
exit()
my_timer.stop('Read all frames')
# Rank the frames by their overall local contrast.
print("+++ Start ranking images")
my_timer.create('Ranking images')
rank_frames = RankFrames(frames, configuration)
rank_frames.frame_score()
my_timer.stop('Ranking images')
print("Index of best frame: " + str(rank_frames.frame_ranks_max_index))
# Initialize the frame alignment object.
align_frames = AlignFrames(frames, rank_frames, configuration)
if configuration.align_frames_mode == "Surface":
my_timer.create('Select optimal alignment patch')
# Select the local rectangular patch in the image where the L gradient is highest in both x
# and y direction. The scale factor specifies how much smaller the patch is compared to the
# whole image frame.
(y_low_opt, y_high_opt, x_low_opt,
x_high_opt) = align_frames.compute_alignment_rect(
configuration.align_frames_rectangle_scale_factor)
my_timer.stop('Select optimal alignment patch')
print("optimal alignment rectangle, y_low: " + str(y_low_opt) +
", y_high: " + str(y_high_opt) + ", x_low: " + str(x_low_opt) +
", x_high: " + str(x_high_opt))
# Align all frames globally relative to the frame with the highest score.
print("+++ Start aligning all frames")
my_timer.create('Global frame alignment')
try:
align_frames.align_frames()
except NotSupportedError as e:
print("Error: " + e.message)
exit()
except InternalError as e:
print("Warning: " + e.message)
my_timer.stop('Global frame alignment')
print("Intersection, y_low: " + str(align_frames.intersection_shape[0][0]) + ", y_high: "
+ str(align_frames.intersection_shape[0][1]) + ", x_low: " \
+ str(align_frames.intersection_shape[1][0]) + ", x_high: " \
+ str(align_frames.intersection_shape[1][1]))
# Compute the average frame.
print("+++ Start computing reference frame")
my_timer.create('Compute reference frame')
average = align_frames.average_frame()
my_timer.stop('Compute reference frame')
print("Reference frame computed from the best " +
str(align_frames.average_frame_number) + " frames.")
# If the ROI is to be set to a smaller size than the whole intersection, do so.
if roi:
print("+++ Start setting ROI and computing new reference frame")
my_timer.create('Setting ROI and new reference')
average_roi = align_frames.set_roi(roi[0], roi[1], roi[2], roi[3])
my_timer.stop('Setting ROI and new reference')
# Initialize the AlignmentPoints object.
my_timer.create('Initialize alignment point object')
alignment_points = AlignmentPoints(configuration, frames, rank_frames,
align_frames)
my_timer.stop('Initialize alignment point object')
if automatic_ap_creation:
# Create alignment points, and create an image with wll alignment point boxes and patches.
print("+++ Start creating alignment points")
my_timer.create('Create alignment points')
# If a ROI is selected, alignment points are created in the ROI window only.
alignment_points.create_ap_grid()
my_timer.stop('Create alignment points')
print("Number of alignment points selected: " +
str(len(alignment_points.alignment_points)) +
", aps dropped because too dim: " +
str(alignment_points.alignment_points_dropped_dim) +
", aps dropped because too little structure: " +
str(alignment_points.alignment_points_dropped_structure))
else:
# Open the alignment point editor.
app = QtWidgets.QApplication(sys.argv)
alignment_point_editor = AlignmentPointEditorWidget(
None, configuration, align_frames, alignment_points, None)
alignment_point_editor.setMinimumSize(800, 600)
alignment_point_editor.showMaximized()
app.exec_()
print("After AP editing, number of APs: " +
str(len(alignment_points.alignment_points)))
count_updates = 0
for ap in alignment_points.alignment_points:
if ap['reference_box'] is not None:
continue
count_updates += 1
AlignmentPoints.set_reference_box(ap, alignment_points.mean_frame)
print("Buffers allocated for " + str(count_updates) +
" alignment points.")
# Produce an overview image showing all alignment points.
if roi:
color_image_with_aps = alignment_points.show_alignment_points(
average_roi)
else:
color_image_with_aps = alignment_points.show_alignment_points(average)
# For each alignment point rank frames by their quality.
my_timer.create('Rank frames at alignment points')
print("+++ Start ranking frames at alignment points")
alignment_points.compute_frame_qualities()
my_timer.stop('Rank frames at alignment points')
# Allocate StackFrames object.
stack_frames = StackFrames(configuration, frames, rank_frames,
align_frames, alignment_points, my_timer)
# Stack all frames.
print("+++ Start stacking frames")
stack_frames.stack_frames()
# Merge the stacked alignment point buffers into a single image.
print("+++ Start merging alignment patches")
stacked_image = stack_frames.merge_alignment_point_buffers()
# If the drizzle factor is 1.5, reduce the pixel resolution of the stacked image buffer
# to half the size used in stacking.
if configuration.drizzle_factor_is_1_5:
print("+++ Start reducing image buffer size")
stack_frames.half_stacked_image_buffer_resolution()
# Save the stacked image as 16bit int (color or mono).
my_timer.create('Saving the final image')
Frames.save_image(stacked_image_name,
stacked_image,
color=frames.color,
header=configuration.global_parameters_version)
my_timer.stop('Saving the final image')
# Print out timer results.
my_timer.stop('Execution over all')
my_timer.print()
# Write the image with alignment points.
Frames.save_image(ap_image_name,
color_image_with_aps,
color=True,
header=configuration.global_parameters_version)
# If a ROI is selected, return both the original and the reduced-size average frame.
if roi:
return average, average_roi, color_image_with_aps, stacked_image
else:
return average, color_image_with_aps, stacked_image
end = time()
print('Elapsed time in computing reference frame: {}'.format(end - start))
print("Reference frame computed from the best " +
str(align_frames.average_frame_number) + " frames.")
# plt.imshow(align_frames.mean_frame, cmap='Greys_r')
# plt.show()
app = QtWidgets.QApplication(argv)
window = AlignmentPointEditorWidget(None, configuration, align_frames,
alignment_points, None)
window.setMinimumSize(800, 600)
window.showMaximized()
app.exec_()
print("After AP editing, number of APs: " +
str(len(alignment_points.alignment_points)) +
", aps dropped because too dim: " +
str(alignment_points.alignment_points_dropped_dim) +
", aps dropped because too little "
"structure: " +
str(alignment_points.alignment_points_dropped_structure))
count_updates = 0
for ap in alignment_points.alignment_points:
if ap['reference_box'] is not None:
continue
count_updates += 1
AlignmentPoints.set_reference_box(ap, align_frames.mean_frame)
print("Buffers allocated for " + str(count_updates) + " alignment points.")
exit()