Cropping images¶
The crop widget allows cropping a 2D or 3D image.
In [1]:
import stackview
from skimage.io import imread
import numpy as np
In [2]:
image = imread("data/CalibZAPWfixed_000154_max.tif")
The widget contains 2 or 3 sliders, for 2D and 3D images respectively. It also supports stackview's typical parameters such as continuous_update, zoom_factor, etc.
In [3]:
image_2d = image[0]
crop_widget_2d = stackview.crop(image_2d, continuous_update=True)
crop_widget_2d
Out[3]:
_Cropper(children=(IntRangeSlider(value=(0, 235), description='Y', max=235), IntRangeSlider(value=(0, 389), de…
In [4]:
crop_widget = stackview.crop(image,
continuous_update=True,
zoom_factor=0.75)
crop_widget
Out[4]:
_Cropper(children=(IntRangeSlider(value=(0, 100), description='Z'), IntRangeSlider(value=(0, 235), description…
You can also modify the labels of the axes. E.g. in the use-case shown here, we're modifying timelapse dataset.
In [5]:
crop_widget = stackview.crop(image,
continuous_update=True,
zoom_factor=0.75,
slider_text="Frame",
axis_names=["Frame", "Y", "X"])
crop_widget
Out[5]:
_Cropper(children=(IntRangeSlider(value=(0, 100), description='Frame'), IntRangeSlider(value=(0, 235), descrip…
Configuring and reading the cropped region¶
You can change the range sliders programmatically.
In [6]:
crop_widget = stackview.crop(image, continuous_update=True, zoom_factor=2)
crop_widget.range = (slice(0, 40), slice(40, 80), slice(80, 120))
crop_widget
Out[6]:
_Cropper(children=(IntRangeSlider(value=(0, 40), description='Z'), IntRangeSlider(value=(40, 80), description=…
You can retrieve the cropped range like this.
In [7]:
r = crop_widget.range
r
Out[7]:
(slice(0, 40, 1), slice(40, 80, 1), slice(80, 120, 1))
It technically is a tuple of Python slices.
In [8]:
r[0].start, r[0].stop
Out[8]:
(0, 40)
Cropping images¶
You can use this range to crop the image...
In [9]:
r = crop_widget.range
image[r].shape
Out[9]:
(40, 40, 40)
... or retrieve the cropped image directly.
In [10]:
cropped_image = crop_widget.crop()
cropped_image.shape
Out[10]:
(40, 40, 40)
This cropped_image object uses stackview's insight under the hood and thus, comes with a nice view.
In [11]:
cropped_image
Out[11]:
|
|
In [12]:
crop_widget = stackview.crop(image,
continuous_update=True,
zoom_factor=0.75)
crop_widget
Out[12]:
_Cropper(children=(IntRangeSlider(value=(0, 100), description='Z'), IntRangeSlider(value=(0, 235), description…
In [13]:
crop_widget.range
Out[13]:
(slice(0, 100, 1), slice(0, 235, 1), slice(0, 389, 1))
In [ ]: