def __init__(self, image_collection, df_positions, pos_columns=['x','y'], tail_length=3, track_column='track'):
CollectionViewer.__init__(self, image_collection)
self.artists = None
self.circle_kwargs = dict(edgecolor='r', radius=6, facecolor=None, fill=False, lw=1)
self.pos_columns = pos_columns
self.track_column = track_column
self.df_positions = df_positions.sort_values(['frame', self.track_column])
image = self.image_collection[0]
# Use the min/max of the first image for all other images
self.vmin_vmax = (np.min(image), np.max(image))
self.tail_length = tail_length
self.traj_colors = ["#ffbfbf", "#ced936", "#3db6f2",
"#6c468c", "#f2553d", "#98b386",
"#566573", "#a336d9", "#7f4840",
"#00ff00", "#0057d9", "#ffbffb",
"#7f3300", "#79f279", "#bfd9ff",
"#f200c2", "#d97736", "#1d7328",
"#1d3473", "#73566d", "#e6cbac",
"#66ccaa", "#7999f2", "#73004d",
"#ffaa00", "#00a7b3", "#0000f2",
"#ff0066", "#73561d", "#bffbff",
"#0000e6", "#d96c98", "#b2a159",
"#004d73", "#3d0073", "#73000f"]
self.traj_colors_len = len(self.traj_colors)
self.update_image(image)
def __init__(self, search_pattern):
bottom_px = 60
self.bottom_px = bottom_px
plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = ['Bottom']
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
plugin += self.show_orig
plugin += ComboBox('setup', self.setup_names)
plugin += Slider('bottom_px',
0,
500,
value=self.bottom_px,
value_type='int')
plugin += Button("Print", callback=self.on_print_click)
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer += plugin
def view(self):
"""Create a matplotlib animated view of the contents.
"""
cv = CollectionViewer(self.images)
cv.show()
return cv
def view(self):
"""Create a matplotlib animated view of the contents.
"""
cv = CollectionViewer(self.images)
cv.show()
return cv
def __init__(self, search_pattern):
blur_kernel_size = 1
cal_fnames = [
path for path in glob.iglob('camera_cal/*.jpg', recursive=True)
]
cal_images, cal_gray_images = read_images(cal_fnames)
self.objpoints, self.imgpoints, _ = get_chessboard_corners(
cal_images, cal_gray_images)
self.blur_kernel_size = blur_kernel_size
self.top_left_x = top_left_x
self.top_left_y = top_left_y
self.top_right_x = top_right_x
self.top_right_y = top_right_y
self.bottom_right_x = bottom_right_x
self.bottom_right_y = bottom_right_y
self.bottom_left_x = bottom_left_x
self.bottom_left_y = bottom_left_y
plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = [
'ROI poly', "ROI Transformation", 'ROI Transformed',
"Final Transformation poly", 'Final Transformation',
'Final Transformed'
]
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
plugin += self.show_orig
plugin += ComboBox('setup', self.setup_names)
plugin += Slider('blur_kernel_size',
0,
31,
value=self.blur_kernel_size,
value_type='int')
plugin += Slider('top_left_x', 0, 1, value=self.top_left_x)
plugin += Slider('top_left_y', 0, 1, value=self.top_left_y)
plugin += Slider('top_right_x', 0, 1, value=self.top_right_x)
plugin += Slider('top_right_y', 0, 1, value=self.top_right_y)
plugin += Slider('bottom_right_x', 0, 1, value=self.bottom_right_x)
plugin += Slider('bottom_right_y', 0, 1, value=self.bottom_right_y)
plugin += Slider('bottom_left_x', 0, 1, value=self.bottom_left_x)
plugin += Slider('bottom_left_y', 0, 1, value=self.bottom_left_y)
plugin += Button("Print", callback=self.on_print_click)
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer += plugin
class CropViewer:
def __init__(self, search_pattern):
bottom_px = 60
self.bottom_px = bottom_px
plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = ['Bottom']
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
plugin += self.show_orig
plugin += ComboBox('setup', self.setup_names)
plugin += Slider('bottom_px',
0,
500,
value=self.bottom_px,
value_type='int')
plugin += Button("Print", callback=self.on_print_click)
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer += plugin
def image_filter(self, image, *args, **kwargs):
print("image: ", image.shape)
show_orig = kwargs["show_orig"]
setup = kwargs["setup"]
self.bottom_px = kwargs["bottom_px"]
if show_orig:
return image
# crop_img = img[200:400, 100:300] # Crop from x, y, w, h -> 100, 200, 300, 400
# NOTE: its img[y: y + h, x: x + w] and *not* img[x: x + w, y: y + h]
result_image = None
if setup == "Bottom":
result_image = apply_crop_bottom(image, bottom_px=self.bottom_px)
return result_image
def on_print_click(self, args):
print("""
bottom_px = {}
""".format(self.bottom_px))
def show(self):
self.viewer.show()
def __init__(self, image_collection, df_positions, pos_columns=['x','y']):
CollectionViewer.__init__(self, image_collection)
self.df_positions = df_positions
self.artists = None
self.circle_kwargs = dict(edgecolor='r', radius=6, facecolor='red', fill=False, lw=1)
self.pos_columns = pos_columns
image = self.image_collection[0]
# Use the min/max of the first image for all other images
self.vmin_vmax = (np.min(image), np.max(image))
self.update_image(image)
def weights_viewer(path):
w = []
for i in range(1000):
filename = "model.ckpt.{:04d}.hdf5".format(i)
m.load_weights(path + filename)
k, b = m.get_weights()
i = np.concatenate((k, np.ones((2,100)), b[None,]))
w.append(i)
CollectionViewer(w).show()
def test_collection_viewer():
img = data.astronaut()
img_collection = tuple(pyramid_gaussian(img, multichannel=True))
view = CollectionViewer(img_collection)
make_key_event(48)
view.update_index('', 2),
assert_equal(view.image, img_collection[2])
view.keyPressEvent(make_key_event(53))
assert_equal(view.image, img_collection[5])
view._format_coord(10, 10)
def test_collection_viewer():
img = data.astronaut()
img_collection = tuple(pyramid_gaussian(img))
view = CollectionViewer(img_collection)
make_key_event(48)
view.update_index('', 2),
assert_equal(view.image, img_collection[2])
view.keyPressEvent(make_key_event(53))
assert_equal(view.image, img_collection[5])
view._format_coord(10, 10)
def testrun():
h_tasks = hierarchical_load('../train/')
print(len(h_tasks))
nsamples = process_the_study(h_tasks[10])
print('We have {} samples'.format(len(nsamples)))
to_show = []
for t in nsamples:
to_show.append(t.imgs[0, :, :])
to_show.append(t.imgs[1, :, :])
to_show.append(t.imgs[10, :, :])
to_show.append(t.imgs[20, :, :])
CollectionViewer(to_show).show()
def show(self):
"""Show the stack of images in a skimage CollectionViewer window"""
#stackims=[self[i] for i in range(len(self))]
cv=CollectionViewer(self)
cv.show()
return cv
import matplotlib.pyplot as plt
folder = r'..\tests\coretestdata\hysteresis_test'
editfolder = r'..\tests\coretestdata\hysteresis_test\edited_ims'
os.chdir(folder)
background = KerrArray('image0000_background.png')
background = background.convert_float()
print 'loading images...'
kl = KerrList('image000*unproccessed.png',
conserve_memory=False,
get_metadata=False)
list(kl) #make sure all images loaded
print 'images loaded'
#%%
print 'convert float'
kl.apply_all('convert_float') #convert pixels to decimal values
print 'correct_drift'
kl.apply_all('correct_drift', ref=background, upsample_factor=200)
print 'subtract'
for i, im in enumerate(kl):
kl[i] = 16 * (kl[i] - background) + 0.5
kl[i] = kl[i].clip_intensity()
#skimage.io.imsave(os.path.join(savefolder,kl.files[i]),kl[i])
print np.array(kl.slice_metadata(key='correct_drift', values_only=True))
cv = CollectionViewer(kl)
cv.show()
"""
=====================
CollectionViewer demo
=====================
Demo of CollectionViewer for viewing collections of images. This demo uses
the different layers of the gaussian pyramid as image collection.
You can scroll through images with the slider, or you can interact with the
viewer using your keyboard:
left/right arrows
Previous/next image in collection.
number keys, 0--9
0% to 90% of collection. For example, "5" goes to the image in the
middle (i.e. 50%) of the collection.
home/end keys
First/last image in collection.
"""
import numpy as np
from skimage import data
from skimage.viewer import CollectionViewer
from skimage.transform import pyramid_gaussian
img = data.lena()
img_collection = tuple(pyramid_gaussian(img))
view = CollectionViewer(img_collection)
view.show()
def __init__(self, search_pattern):
self.plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = ['Yellow', 'White', 'Yellow / White']
self.color_spaces = ['LAB', 'HSV', 'HLS', 'LUV']
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
self.plugin += self.show_orig
self.setup = ComboBox('setup', self.setup_names)
self.color_space = ComboBox('color_space', self.color_spaces)
self.sensity_range = Slider('sensity_range',
10,
100,
value=sensity_range,
value_type='int')
self.lower_yellow_1 = Slider('lower_yellow_1',
0,
255,
value=lower_yellow_1,
value_type='int')
self.lower_yellow_2 = Slider('lower_yellow_2',
0,
255,
value=lower_yellow_2,
value_type='int')
self.lower_yellow_3 = Slider('lower_yellow_3',
0,
255,
value=lower_yellow_3,
value_type='int')
self.upper_yellow_1 = Slider('upper_yellow_1',
0,
255,
value=upper_yellow_1,
value_type='int')
self.upper_yellow_2 = Slider('upper_yellow_2',
0,
255,
value=upper_yellow_2,
value_type='int')
self.upper_yellow_3 = Slider('upper_yellow_3',
0,
255,
value=upper_yellow_3,
value_type='int')
self.lower_white_1 = Slider('lower_white_1',
0,
255,
value=lower_white_1,
value_type='int')
self.lower_white_2 = Slider('lower_white_2',
0,
255,
value=lower_white_2,
value_type='int')
self.lower_white_3 = Slider('lower_white_3',
0,
255,
value=lower_white_3,
value_type='int')
self.upper_white_1 = Slider('upper_white_1',
0,
255,
value=upper_white_1,
value_type='int')
self.upper_white_2 = Slider('upper_white_2',
0,
255,
value=upper_white_2,
value_type='int')
self.upper_white_3 = Slider('upper_white_3',
0,
255,
value=upper_white_3,
value_type='int')
self.plugin += self.setup
self.plugin += self.color_space
# self.plugin += self.sensity_range
self.plugin += self.lower_yellow_1
self.plugin += self.lower_yellow_2
self.plugin += self.lower_yellow_3
self.plugin += self.upper_yellow_1
self.plugin += self.upper_yellow_2
self.plugin += self.upper_yellow_3
self.plugin += self.lower_white_1
self.plugin += self.lower_white_2
self.plugin += self.lower_white_3
self.plugin += self.upper_white_1
self.plugin += self.upper_white_2
self.plugin += self.upper_white_3
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer.connect_event('button_press_event', self.on_filter_color)
self.viewer.connect_event('key_press_event', self.on_press)
self.viewer += self.plugin
class ColorViewer:
def __init__(self, search_pattern):
self.plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = ['Yellow', 'White', 'Yellow / White']
self.color_spaces = ['LAB', 'HSV', 'HLS', 'LUV']
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
self.plugin += self.show_orig
self.setup = ComboBox('setup', self.setup_names)
self.color_space = ComboBox('color_space', self.color_spaces)
self.sensity_range = Slider('sensity_range',
10,
100,
value=sensity_range,
value_type='int')
self.lower_yellow_1 = Slider('lower_yellow_1',
0,
255,
value=lower_yellow_1,
value_type='int')
self.lower_yellow_2 = Slider('lower_yellow_2',
0,
255,
value=lower_yellow_2,
value_type='int')
self.lower_yellow_3 = Slider('lower_yellow_3',
0,
255,
value=lower_yellow_3,
value_type='int')
self.upper_yellow_1 = Slider('upper_yellow_1',
0,
255,
value=upper_yellow_1,
value_type='int')
self.upper_yellow_2 = Slider('upper_yellow_2',
0,
255,
value=upper_yellow_2,
value_type='int')
self.upper_yellow_3 = Slider('upper_yellow_3',
0,
255,
value=upper_yellow_3,
value_type='int')
self.lower_white_1 = Slider('lower_white_1',
0,
255,
value=lower_white_1,
value_type='int')
self.lower_white_2 = Slider('lower_white_2',
0,
255,
value=lower_white_2,
value_type='int')
self.lower_white_3 = Slider('lower_white_3',
0,
255,
value=lower_white_3,
value_type='int')
self.upper_white_1 = Slider('upper_white_1',
0,
255,
value=upper_white_1,
value_type='int')
self.upper_white_2 = Slider('upper_white_2',
0,
255,
value=upper_white_2,
value_type='int')
self.upper_white_3 = Slider('upper_white_3',
0,
255,
value=upper_white_3,
value_type='int')
self.plugin += self.setup
self.plugin += self.color_space
# self.plugin += self.sensity_range
self.plugin += self.lower_yellow_1
self.plugin += self.lower_yellow_2
self.plugin += self.lower_yellow_3
self.plugin += self.upper_yellow_1
self.plugin += self.upper_yellow_2
self.plugin += self.upper_yellow_3
self.plugin += self.lower_white_1
self.plugin += self.lower_white_2
self.plugin += self.lower_white_3
self.plugin += self.upper_white_1
self.plugin += self.upper_white_2
self.plugin += self.upper_white_3
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer.connect_event('button_press_event', self.on_filter_color)
self.viewer.connect_event('key_press_event', self.on_press)
self.viewer += self.plugin
def on_filter_color(self, event):
if event.inaxes and event.inaxes.get_navigate():
self.viewer.status_message(
self.format_coord(event.xdata, event.ydata))
else:
self.viewer.status_message('')
def format_coord(self, x, y):
x = int(x + 0.5)
y = int(y + 0.5)
pixel = self.viewer.image[y, x]
lower_lst = [
pixel[0] - self.sensity_range.val,
pixel[1] - self.sensity_range.val,
pixel[2] - self.sensity_range.val
]
upper_lst = [
pixel[0] + self.sensity_range.val,
pixel[1] + self.sensity_range.val,
pixel[2] + self.sensity_range.val
]
setup = self.setup.val
if setup == "Yellow":
self.update_yellow_params(*lower_lst, *upper_lst)
elif setup == "White":
self.update_white_params(*lower_lst, *upper_lst)
else:
print("Select only one color!")
def update_yellow_params(self, lower1, lower2, lower3, upper1, upper2,
upper3):
lower1 = self.update_val(self.lower_yellow_1, lower1)
lower2 = self.update_val(self.lower_yellow_2, lower2)
lower3 = self.update_val(self.lower_yellow_3, lower3)
upper1 = self.update_val(self.upper_yellow_1, upper1)
upper2 = self.update_val(self.upper_yellow_2, upper2)
upper3 = self.update_val(self.upper_yellow_3, upper3)
self.plugin.filter_image()
def update_white_params(self, lower1, lower2, lower3, upper1, upper2,
upper3):
lower1 = self.update_val(self.lower_white_1, lower1)
lower2 = self.update_val(self.lower_white_2, lower2)
lower3 = self.update_val(self.lower_white_3, lower3)
upper1 = self.update_val(self.upper_white_1, upper1)
upper2 = self.update_val(self.upper_white_2, upper2)
upper3 = self.update_val(self.upper_white_3, upper3)
self.plugin.filter_image()
def image_filter(self, image, *args, **kwargs):
print("image: ", image.shape)
image = apply_crop_bottom(image)
# print("cropped image: ", image.shape)
image, M, Minv = apply_warp(image)
# print("warped image: ", image.shape)
show_orig = kwargs["show_orig"]
setup = kwargs["setup"]
color_space = kwargs["color_space"]
lower_yellow_1 = kwargs["lower_yellow_1"]
lower_yellow_2 = kwargs["lower_yellow_2"]
lower_yellow_3 = kwargs["lower_yellow_3"]
upper_yellow_1 = kwargs["upper_yellow_1"]
upper_yellow_2 = kwargs["upper_yellow_2"]
upper_yellow_3 = kwargs["upper_yellow_3"]
lower_white_1 = kwargs["lower_white_1"]
lower_white_2 = kwargs["lower_white_2"]
lower_white_3 = kwargs["lower_white_3"]
upper_white_1 = kwargs["upper_white_1"]
upper_white_2 = kwargs["upper_white_2"]
upper_white_3 = kwargs["upper_white_3"]
if show_orig:
return image
lower_yellow = np.array(
[lower_yellow_1, lower_yellow_2, lower_yellow_3])
upper_yellow = np.array(
[upper_yellow_1, upper_yellow_2, upper_yellow_3])
lower_white = np.array([lower_white_1, lower_white_2, lower_white_3])
upper_white = np.array([upper_white_1, upper_white_2, upper_white_3])
target_color_space = cv2.COLOR_RGB2HSV
if color_space == "LAB":
target_color_space = cv2.COLOR_RGB2Lab
elif color_space == "HLS":
target_color_space = cv2.COLOR_RGB2HLS
elif color_space == "LUV":
target_color_space = cv2.COLOR_RGB2LUV
result_image = None
if setup == "Yellow":
result_image = filter_color(image,
lower_yellow,
upper_yellow,
trg_color_space=target_color_space)
elif setup == "White":
result_image = filter_color(image,
lower_white,
upper_white,
trg_color_space=target_color_space)
elif setup == "Yellow / White":
result_yellow = filter_color(image,
lower_yellow,
upper_yellow,
trg_color_space=target_color_space)
result_white = filter_color(image,
lower_white,
upper_white,
trg_color_space=target_color_space)
result_image = cv2.bitwise_or(result_yellow, result_white)
return result_image
def on_press(self, event):
if event.key == 'ctrl+r':
self.on_reset()
elif event.key == 'ctrl+p':
self.on_print()
def on_print(self, args=None):
print("""
lower_yellow_1 = {}
lower_yellow_2 = {}
lower_yellow_3 = {}
upper_yellow_1 = {}
upper_yellow_2 = {}
upper_yellow_3 = {}
lower_white_1 = {}
lower_white_2 = {}
lower_white_3 = {}
upper_white_1 = {}
upper_white_2 = {}
upper_white_3 = {}
""".format(
self.lower_yellow_1.val, self.lower_yellow_2.val,
self.lower_yellow_3.val, self.upper_yellow_1.val,
self.upper_yellow_2.val, self.upper_yellow_3.val,
self.lower_white_1.val, self.lower_white_2.val,
self.lower_white_3.val, self.upper_white_1.val,
self.upper_white_2.val, self.upper_white_3.val))
def on_reset(self, args=None):
self.update_val(self.lower_yellow_1, lower_yellow_1)
self.update_val(self.lower_yellow_2, lower_yellow_2)
self.update_val(self.lower_yellow_3, lower_yellow_3)
self.update_val(self.upper_yellow_1, upper_yellow_1)
self.update_val(self.upper_yellow_2, upper_yellow_2)
self.update_val(self.upper_yellow_3, upper_yellow_3)
self.update_val(self.lower_white_1, lower_white_1)
self.update_val(self.lower_white_2, lower_white_2)
self.update_val(self.lower_white_3, lower_white_3)
self.update_val(self.upper_white_1, upper_white_1)
self.update_val(self.upper_white_2, upper_white_2)
self.update_val(self.upper_white_3, upper_white_3)
self.plugin.filter_image()
def update_val(self, comp, newval, min_val=0, max_val=255):
newval = max(0, newval)
newval = min(255, newval)
comp.val = newval
comp.editbox.setText("%s" % newval)
return newval
def show(self):
self.viewer.show()
def show_image_collection(im3d):
viewer3d = CollectionViewer(im3d)
viewer3d.show()
"""
=====================
CollectionViewer demo
=====================
Demo of CollectionViewer for viewing collections of images. This demo uses
the different layers of the gaussian pyramid as image collection.
You can scroll through images with the slider, or you can interact with the
viewer using your keyboard:
left/right arrows
Previous/next image in collection.
number keys, 0--9
0% to 90% of collection. For example, "5" goes to the image in the
middle (i.e. 50%) of the collection.
home/end keys
First/last image in collection.
"""
from skimage import data
from skimage.viewer import CollectionViewer
from skimage.transform import pyramid_gaussian
img = data.astronaut()
img_collection = tuple(pyramid_gaussian(img))
view = CollectionViewer(img_collection)
view.show()
#!/usr/bin/env python
import numpy as np
import skimage.io as io
from skimage.viewer import CollectionViewer
import cremi.evaluation as evaluation
import cremi.io.CremiFile as CremiFile
if __name__ == "__main__":
img = [io.imread('example.png')]
for w in (0, 2, 4, 10):
target = np.copy(img[0])[...,np.newaxis]
evaluation.create_border_mask(img[0][...,np.newaxis],target,w,105,axis=2)
img.append(target[...,0])
v = CollectionViewer(img)
v.show()
cfIn = CremiFile('example.h5', 'r')
cfOut = CremiFile('output.h5', 'a')
evaluation.create_and_write_masked_neuron_ids(cfIn, cfOut, 3, 240, overwrite=True)
==================================
Demo of a CollectionViewer for viewing collections of images with the
`autolevel` rank filter connected as a plugin.
"""
from skimage import data
from skimage.filter import rank
from skimage.morphology import disk
from skimage.viewer import CollectionViewer
from skimage.viewer.widgets import Slider
from skimage.viewer.plugins.base import Plugin
# Wrap autolevel function to make the disk size a filter argument.
def autolevel(image, disk_size):
return rank.autolevel(image, disk(disk_size))
img_collection = [data.camera(), data.coins(), data.text()]
plugin = Plugin(image_filter=autolevel)
plugin += Slider("disk_size", 2, 8, value_type="int")
plugin.name = "Autolevel"
viewer = CollectionViewer(img_collection)
viewer += plugin
viewer.show()
class RoiViewer:
def __init__(self, search_pattern):
blur_kernel_size = 1
cal_fnames = [
path for path in glob.iglob('camera_cal/*.jpg', recursive=True)
]
cal_images, cal_gray_images = read_images(cal_fnames)
self.objpoints, self.imgpoints, _ = get_chessboard_corners(
cal_images, cal_gray_images)
self.blur_kernel_size = blur_kernel_size
self.top_left_x = top_left_x
self.top_left_y = top_left_y
self.top_right_x = top_right_x
self.top_right_y = top_right_y
self.bottom_right_x = bottom_right_x
self.bottom_right_y = bottom_right_y
self.bottom_left_x = bottom_left_x
self.bottom_left_y = bottom_left_y
plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = [
'ROI poly', "ROI Transformation", 'ROI Transformed',
"Final Transformation poly", 'Final Transformation',
'Final Transformed'
]
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
plugin += self.show_orig
plugin += ComboBox('setup', self.setup_names)
plugin += Slider('blur_kernel_size',
0,
31,
value=self.blur_kernel_size,
value_type='int')
plugin += Slider('top_left_x', 0, 1, value=self.top_left_x)
plugin += Slider('top_left_y', 0, 1, value=self.top_left_y)
plugin += Slider('top_right_x', 0, 1, value=self.top_right_x)
plugin += Slider('top_right_y', 0, 1, value=self.top_right_y)
plugin += Slider('bottom_right_x', 0, 1, value=self.bottom_right_x)
plugin += Slider('bottom_right_y', 0, 1, value=self.bottom_right_y)
plugin += Slider('bottom_left_x', 0, 1, value=self.bottom_left_x)
plugin += Slider('bottom_left_y', 0, 1, value=self.bottom_left_y)
plugin += Button("Print", callback=self.on_print_click)
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer += plugin
def image_filter(self, image, *args, **kwargs):
print("image: ", image.shape)
image = correct_distortion(image, self.objpoints, self.imgpoints)
print("undistorted image: ", image.shape)
image = apply_crop_bottom(image)
print("cropped image: ", image.shape)
show_orig = kwargs["show_orig"]
setup = kwargs["setup"]
self.blur_kernel_size = kwargs["blur_kernel_size"]
self.top_left_x = kwargs["top_left_x"]
self.top_left_y = kwargs["top_left_y"]
self.top_right_x = kwargs["top_right_x"]
self.top_right_y = kwargs["top_right_y"]
self.bottom_right_x = kwargs["bottom_right_x"]
self.bottom_right_y = kwargs["bottom_right_y"]
self.bottom_left_x = kwargs["bottom_left_x"]
self.bottom_left_y = kwargs["bottom_left_y"]
if show_orig:
return image
height, width = image.shape[:2]
src_top_left = (width * self.top_left_x, height * self.top_left_y)
src_top_right = (width * self.top_right_x, height * self.top_right_y)
src_bottom_right = (width * self.bottom_right_x,
height * self.bottom_right_y)
src_bottom_left = (width * self.bottom_left_x,
height * self.bottom_left_y)
trg_top_left = (width * self.bottom_left_x, 0)
trg_top_right = (width * self.bottom_right_x, 0)
trg_bottom_right = (width * self.bottom_right_x,
height * self.bottom_right_y)
trg_bottom_left = (width * self.bottom_left_x,
height * self.bottom_left_y)
result_image = image
if setup == "ROI poly":
vertices = np.array([[
src_top_left, src_top_right, src_bottom_right, src_bottom_left
]],
dtype=np.int32)
cv2.polylines(result_image, [vertices],
isClosed=True,
color=(0, 255, 255),
thickness=2)
elif setup == "ROI Transformation":
vertices = np.array([[
trg_top_left, trg_top_right, trg_bottom_right, trg_bottom_left
]],
dtype=np.int32)
cv2.polylines(result_image, [vertices],
isClosed=True,
color=(0, 255, 255),
thickness=2)
elif setup == "ROI Transformed":
src = np.float32([
src_top_left, src_top_right, src_bottom_right, src_bottom_left
])
trg = np.float32([
trg_top_left, trg_top_right, trg_bottom_right, trg_bottom_left
])
result_image, M, Minv = warp_image(result_image, src, trg)
elif setup == "Final Transformation poly":
result_image = apply_color_and_threshold(image) * 255
vertices = np.array([[
src_top_left, src_top_right, src_bottom_right, src_bottom_left
]],
dtype=np.int32)
cv2.polylines(result_image, [vertices],
isClosed=True,
color=(255, 255, 255),
thickness=2)
elif setup == "Final Transformation":
result_image = apply_color_and_threshold(image) * 255
vertices = np.array([[
trg_top_left, trg_top_right, trg_bottom_right, trg_bottom_left
]],
dtype=np.int32)
cv2.polylines(result_image, [vertices],
isClosed=True,
color=(255, 255, 255),
thickness=2)
elif setup == "Final Transformed":
src = np.float32([
src_top_left, src_top_right, src_bottom_right, src_bottom_left
])
trg = np.float32([
trg_top_left, trg_top_right, trg_bottom_right, trg_bottom_left
])
result_image, M, Minv = warp_image(image, src, trg)
result_image = apply_color_and_threshold(result_image) * 255
return result_image
def on_print_click(self, args):
print("""
blur_kernel_size = {}
top_left_x = {}
top_left_y = {}
top_right_x = {}
top_right_y = {}
bottom_right_x = {}
bottom_right_y = {}
bottom_left_x = {}
bottom_left_y = {}
""".format(self.blur_kernel_size, self.top_left_x, self.top_left_y,
self.top_right_x, self.top_right_y, self.bottom_right_x,
self.bottom_right_y, self.bottom_left_x,
self.bottom_left_y))
def show(self):
self.viewer.show()
from skimage import morphology from scipy import ndimage as ndi from skimage.viewer import ImageViewer from skimage.viewer import CollectionViewer import numpy as np im3d = np.random.rand(100, 100, 100) viewer3d = CollectionViewer(im3d) viewer3d.show()
return util.img_as_ubyte(io.imread(f), force_copy=True)
slice_collection = io.ImageCollection(path.join(SLICE_DIR, SLICE_PATTERN),
load_func=load_uint8)
vol_img = slice_collection.concatenate()
img_otsu = otsu(vol_img)
save_samples('otsu_mask_initial', red_overlay(vol_img, img_otsu))
save_samples('otsu_initial', img_otsu)
# img_sobel = slice_by_slice(sobel_edges, vol_img, datatype=np.float)
# img_binary = img_sobel > EDGE_THRESHOLD
# save_samples('sobel', img_sobel)
# save_samples('sobel_binary', img_binary)
# save_samples('sobel_overlay', red_overlay(vol_img, img_binary))
img_binary = slice_by_slice(fill_interior, img_otsu)
save_samples('filled', red_overlay(vol_img, img_binary))
img_binary = slice_by_slice(erode_to_infill, img_binary)
save_samples('eroded', red_overlay(vol_img, img_binary))
img_binary[28:84, :, :] = 0
percentage = 100 * np.sum(img_otsu & img_binary) / np.sum(img_binary)
print('Infill percentage: {0} %'.format(percentage))
viewer = CollectionViewer(red_overlay(vol_img, img_binary))
viewer.show()
def __init__(self, search_pattern):
plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = [
'Sobel Thresh X', 'Sobel Thresh Y', 'Sobel Thresh X / Y',
'Magnitude Thresh', 'Gradient Direction',
'Magnitude / Gradient Direction Thresh', "2 & 2", "2 | 2"
]
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
plugin += self.show_orig
plugin += ComboBox('setup', self.setup_names)
plugin += Slider('grad_ksize',
0,
31,
value=grad_ksize,
value_type='int')
plugin += Slider('grad_thresh_low',
0,
255,
value=grad_thresh_low,
value_type='int')
plugin += Slider('grad_thresh_high',
0,
255,
value=grad_thresh_high,
value_type='int')
plugin += Slider('mag_binary_ksize',
0,
31,
value=mag_binary_ksize,
value_type='int')
plugin += Slider('mag_binary_thresh_low',
0,
255,
value=mag_binary_thresh_low,
value_type='int')
plugin += Slider('mag_binary_thresh_high',
0,
255,
value=mag_binary_thresh_high,
value_type='int')
plugin += Slider('dir_binary_ksize',
0,
31,
value=dir_binary_ksize,
value_type='int')
plugin += Slider('dir_binary_thresh_low',
0,
np.pi,
value=dir_binary_thresh_low)
plugin += Slider('dir_binary_thresh_high',
0,
np.pi,
value=dir_binary_thresh_high)
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer += plugin
class ThreshViewer:
def __init__(self, search_pattern):
plugin = Plugin(image_filter=self.image_filter, dock="right")
self.setup_names = [
'Sobel Thresh X', 'Sobel Thresh Y', 'Sobel Thresh X / Y',
'Magnitude Thresh', 'Gradient Direction',
'Magnitude / Gradient Direction Thresh', "2 & 2", "2 | 2"
]
self.show_orig = CheckBox('show_orig', value=False, alignment='left')
plugin += self.show_orig
plugin += ComboBox('setup', self.setup_names)
plugin += Slider('grad_ksize',
0,
31,
value=grad_ksize,
value_type='int')
plugin += Slider('grad_thresh_low',
0,
255,
value=grad_thresh_low,
value_type='int')
plugin += Slider('grad_thresh_high',
0,
255,
value=grad_thresh_high,
value_type='int')
plugin += Slider('mag_binary_ksize',
0,
31,
value=mag_binary_ksize,
value_type='int')
plugin += Slider('mag_binary_thresh_low',
0,
255,
value=mag_binary_thresh_low,
value_type='int')
plugin += Slider('mag_binary_thresh_high',
0,
255,
value=mag_binary_thresh_high,
value_type='int')
plugin += Slider('dir_binary_ksize',
0,
31,
value=dir_binary_ksize,
value_type='int')
plugin += Slider('dir_binary_thresh_low',
0,
np.pi,
value=dir_binary_thresh_low)
plugin += Slider('dir_binary_thresh_high',
0,
np.pi,
value=dir_binary_thresh_high)
fnames = [path for path in glob.iglob(search_pattern, recursive=True)]
images, gray_images = read_images(fnames)
self.viewer = CollectionViewer(images)
self.viewer += plugin
def image_filter(self, image, *args, **kwargs):
print("image: ", image.shape)
image = apply_crop_bottom(image)
print("cropped image: ", image.shape)
image, M, Minv = apply_warp(image)
print("warped image: ", image.shape)
show_orig = kwargs["show_orig"]
setup = kwargs["setup"]
grad_ksize = kwargs["grad_ksize"]
grad_thresh_low = kwargs["grad_thresh_low"]
grad_thresh_high = kwargs["grad_thresh_high"]
mag_binary_ksize = kwargs["mag_binary_ksize"]
mag_binary_thresh_low = kwargs["mag_binary_thresh_low"]
mag_binary_thresh_high = kwargs["mag_binary_thresh_high"]
dir_binary_ksize = kwargs["dir_binary_ksize"]
dir_binary_thresh_low = kwargs["dir_binary_thresh_low"]
dir_binary_thresh_high = kwargs["dir_binary_thresh_high"]
if show_orig:
# return apply_color_and_threshold(image) * 255
return image
gradx = abs_sobel_thresh(image,
orient='x',
sobel_kernel=grad_ksize,
thresh=(grad_thresh_low, grad_thresh_high),
rgb2gray=False)
grady = abs_sobel_thresh(image,
orient='y',
sobel_kernel=grad_ksize,
thresh=(grad_thresh_low, grad_thresh_high),
rgb2gray=False)
mag_binary = mag_thresh(image,
sobel_kernel=mag_binary_ksize,
thresh=(mag_binary_thresh_low,
mag_binary_thresh_high),
rgb2gray=False)
dir_binary = dir_threshold(image,
sobel_kernel=dir_binary_ksize,
thresh=(dir_binary_thresh_low,
dir_binary_thresh_high),
rgb2gray=False)
combined_sobel = np.zeros_like(gradx)
combined_sobel[((gradx == 1) & (grady == 1))] = 1
combined_magn_grad = np.zeros_like(mag_binary)
combined_magn_grad[((mag_binary == 1) & (dir_binary == 1))] = 1
result_image = None
if setup == "Sobel Thresh X":
result_image = gradx
elif setup == "Sobel Thresh Y":
result_image = grady
elif setup == "Sobel Thresh X / Y":
result_image = combined_sobel
elif setup == "Magnitude Thresh":
result_image = mag_binary
elif setup == "Gradient Direction":
result_image = dir_binary
elif setup == "Magnitude / Gradient Direction Thresh":
result_image = combined_magn_grad
elif setup == "2 & 2":
result_image = np.zeros_like(combined_sobel)
result_image[((combined_sobel == 1) &
(combined_magn_grad == 1))] = 1
elif setup == "2 | 2":
result_image = np.zeros_like(combined_sobel)
result_image[((combined_sobel == 1) |
(combined_magn_grad == 1))] = 1
return result_image
def show(self):
self.viewer.show()