Skip to content

Commit

Permalink
allow cropping in data units
Browse files Browse the repository at this point in the history
  • Loading branch information
@MaartenBransen
MaartenBransen committed Oct 25, 2023
1 parent b0de76c commit 7058b65
Show file tree
Hide file tree
Showing 3 changed files with 230 additions and 15 deletions.
18 changes: 18 additions & 0 deletions scm_confocal/sp8.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -995,6 +995,15 @@ def export_with_scalebar(self,frame=0,channel=0,filename=None,**kwargs):
optional rescaling using `resolution`).
The default is `None` which takes the entire image.
crop_unit : `'pixels'` or `'data'`, optional
sets the unit in which the width and height in `crop` are
specified when using the (x,y,w,h) format, with `'pixels'` to give
the size in pixels or `'data'` to specify the size in the physical
unit used for the scalebar (after optional unit conversion via the
`convert` parameter). Note that the position of the top left corner
is given in pixels. The `((xmin,ymin),(xmax,ymax))` format must be
always given in pixels, and `crop_unit` is ignored if `crop` is
given in this format. The default is `'pixels'`.
resolution : int, optional
the resolution along the x-axis (i.e. image width in pixels) to use
for the exported image. The default is `None`, which uses the size
Expand Down Expand Up @@ -1801,6 +1810,15 @@ def export_with_scalebar(self,frame=0,channel=0,filename=None,**kwargs):
optional rescaling using `resolution`).
The default is `None` which takes the entire image.
crop_unit : `'pixels'` or `'data'`, optional
sets the unit in which the width and height in `crop` are
specified when using the (x,y,w,h) format, with `'pixels'` to give
the size in pixels or `'data'` to specify the size in the physical
unit used for the scalebar (after optional unit conversion via the
`convert` parameter). Note that the position of the top left corner
is given in pixels. The `((xmin,ymin),(xmax,ymax))` format must be
always given in pixels, and `crop_unit` is ignored if `crop` is
given in this format. The default is `'pixels'`.
resolution : int, optional
the resolution along the x-axis (i.e. image width in pixels) to use
for the exported image. The default is `None`, which uses the size
Expand Down
209 changes: 194 additions & 15 deletions scm_confocal/util.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import numpy as np
from warnings import warn

def align_stack(images,startim=0,threshold=0,binning=1,smooth=0,upsample=1,
startoffset=(0,0),trim=True,blocksize=None,
Expand Down Expand Up @@ -1620,14 +1621,174 @@ def _get_pure_cmap(name):
return cmap

def _export_with_scalebar(exportim,pixelsize,unit,filename,multichannel,
crop=None,resolution=None,cmap='inferno',cmap_range=None,draw_bar=True,
barsize=None,scale=1,loc=2,convert=None,barcolor=(255,255,255),
barthickness=14,barpad=10,draw_text=True,text=None,font='arialbd.ttf',
fontsize=16,fontcolor=(255,255,255),fontbaseline=10,fontpad=10,
draw_box=False,boxcolor=(0,0,0),boxopacity=255,boxpad=10,save=True,
show_figure=True,store_settings=False,preprocess=None,pixel_aspect=None):
crop=None,crop_unit='pixels',resolution=None,cmap='inferno',
cmap_range=None,draw_bar=True,barsize=None,scale=1,loc=2,convert=None,
barcolor=(255,255,255),barthickness=14,barpad=10,draw_text=True,
text=None,font='arialbd.ttf',fontsize=16,fontcolor=(255,255,255),
fontbaseline=10,fontpad=10,draw_box=False,boxcolor=(0,0,0),
boxopacity=255,boxpad=10,save=True,show_figure=True,
store_settings=False,preprocess=None,pixel_aspect=None):
"""
see top level export_with_scalebar functions for docs
for exporting a scale bar, generally to be called from top level microscope
classes.
Parameters
----------
exportim : 2D numpy.ndarray or list thereof
the image data of the image to export, or a list of arrays for multiple
image channels
pixelsize : float
physical size of the pixels in exportim
unit : str
unit of the pixelsize
filename : string
Filename + extension to use for the export file.
multichannel : bool
whether the data consists of multiple image channels
crop : tuple or `None`, optional
range describing a area of the original image (before rescaling the
resolution) to crop out for the export image. Can have two forms:
- `((xmin,ymin),(xmax,ymax))`, with the integer indices of the top
left and bottom right corners respectively.
- `(xmin,ymin,w,h)` with the integer indices of the top left corner
and the width and heigth of the cropped image in pixels (prior to
optional rescaling using `resolution`).
The default is `None` which takes the entire image.
crop_unit : `'pixels'` or `'data'`, optional
sets the unit in which the width and height in `crop` are
specified when using the (x,y,w,h) format, with `'pixels'` to give
the size in pixels or `'data'` to specify the size in the physical
unit used for the scalebar (after optional unit conversion via the
`convert` parameter). Note that the position of the top left corner
is given in pixels. The `((xmin,ymin),(xmax,ymax))` format must be
always given in pixels, and `crop_unit` is ignored if `crop` is
given in this format. The default is `'pixels'`.
resolution : int, optional
the resolution along the x-axis (i.e. image width in pixels) to use
for the exported image. The default is `None`, which uses the size
of the original image (after optional cropping using `crop`).
cmap : str or callable or list of str or list of callable, optional
name of a named Matplotlib colormap used to color the data. see the
[Matplotlib documentation](
https://matplotlib.org/stable/tutorials/colors/colormaps.html)
for more information. The default is `'inferno'`.
In addition to the colormaps listed there, the following maps for
linearly incrementing pure RGB channels are available, useful for
e.g. displaying multichannel data with complementary colors (no
overlap between between colormaps possible):
```
['pure_reds', 'pure_greens', 'pure_blues', 'pure_yellows',
'pure_cyans', 'pure_purples','pure_greys']
```
where for example `'pure_reds'` scales between RGB values `(0,0,0)`
and `(255,0,0)`, and `'pure_cyans'` between `(0,0,0)` and
`(0,255,255)`.
Alternatively, a fully custom colormap may be used by entering a
[ListedColormap](https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.ListedColormap.html#matplotlib.colors.ListedColormap)
or [LinearSegmentedColormap](https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.LinearSegmentedColormap.html#matplotlib.colors.LinearSegmentedColormap)
object from the Matplotlib.colors module. For more information on
creating colormaps, see the Matplotlib documentation linked above.
For multichannel data, a list of colormaps *must* be provided, with
a separate colormap for each channel.
cmap_range : tuple of form (min,max) or None or `'automatic'`, optional
sets the scaling of the colormap. The minimum and maximum
values to map the colormap to, values outside of this range will
be colored according to the min and max value of the colormap. The
default is `None`, which is to take the lowest and highest value
in the image. Alternatively `'automatic'` may be specified which
scales between the 10th and 99th percentile. For multichannel data
a list of cmap_range options per channel may be provided.
draw_bar : boolean, optional
whether to draw a scalebar on the image, such that this function
may be used to put other text on the image or just to apply a
colormap (by setting `draw_bar=False` and `draw_text=False`). The
default is `True`.
barsize : float or `None`, optional
size (in data units matching the original scale bar, e.g. nm) of
the scale bar to use. The default `None`, wich takes the desired
length for the current scale (ca. 15% of the width of the image for
`scale=1`) and round this to the nearest option from a list of
"nice" values.
scale : float, optional
factor to change the size of the scalebar+text with respect to the
width of the image. Scale is chosen such, that at `scale=1` the
font size of the scale bar text is approximately 10 pt when
the image is printed at half the width of the text in a typical A4
paper document (e.g. two images side-by-side). Note that this is
with respect to the **output** image, so after optional cropping
and/or up/down sampling has been applied. The default is `1`.
loc : int, one of [`0`,`1`,`2`,`3`], optional
Location of the scalebar on the image, where `0`, `1`, `2` and `3`
refer to the top left, top right, bottom left and bottom right
respectively. The default is `2`, which is the bottom left corner.
convert : str, one of [`'fm'`,`'pm'`,`'Å'` or `A`,`'nm'`,`'µm'` or `'um'`,`'mm'`,`'cm'`,`'dm'`,`'m'`], optional
Unit that will be used for the scale bar, the value will be
automatically converted if this unit differs from the pixel size
unit. The default is `None`, which uses micrometers.
barcolor : tuple of ints, optional
RGB color to use for the scalebar and text, given as a tuple of
form (R,G,B) or (R,G,B,A) where R, G B and A are values between 0
and 255 for red, green, blue and alpha respectively. The default is
`(255,255,255)`, which gives a white scalebar.
barthickness : int, optional
thickness in printer points of the scale bar itself. The default is
16.
barpad : int, optional
size in printer points of the padding between the scale bar and the
surrounding box. The default is 10.
draw_text : bool, optional
whether to draw the text specified in `text` on the image, the text
is place above the scale bar if `draw_bar=True`. The default is
`True`.
text : str, optional
the text to draw on the image (above the scale bar if
`draw_bar=True`). The default is `None`, which gives the size and
unit of the scale bar (e.g. `'10 µm'`).
font : str, optional
filename of an installed TrueType font ('.ttf' file) to use for the
text on the scalebar. The default is `'arialbd.ttf'`.
fontsize : int, optional
base font size to use for the scale bar text. The default is 16.
Note that this size will be re-scaled according to `resolution` and
`scale`.
fontcolor : tuple of int, optional
(R,G,B) tuple where R, G and B are red, green and blue values from
0 to 255. The default is (255,255,255) giving white text.
fontbaseline : int, optional
vertical offset for the baseline of the scale bar text in from the
top of the scale bar in printer points. The default is 10.
fontpad : int, optional
minimum size in printer points of the space/padding between the
text and surrounding box. The default is 10.
draw_box : bool, optional
Whether to put a colored box behind the scalebar and text to
enhance contrast on busy images. The default is `False`.
boxcolor : tuple of ints, optional
RGB color to use for the box behind/around the scalebar and text,
given as a tuple of form (R,G,B) or (R,G,B,A) where R, G B and A
are values between 0 and 255 for red, green and blue respectively.
If no A is given, `boxopacity` is used. The default is (0,0,0)
which gives a black box.
boxopacity : int, optional
value between 0 and 255 for the opacity/alpha of the box, useful
for creating a semitransparent box. The default is 255.
boxpad : int, optional
size of the space/padding around the box (with respect to the sides
of the image) in printer points. The default is 10.
save : bool, optional
whether to save the image as file. The default is True.
show_figure : bool, optional
whether to open matplotlib figure windows. The default is True.
Returns
-------
Y×X×4 numpy.array containing the BGRA pixel data
"""
#store all settings from locals before anything is changed or loaded
if store_settings:
Expand Down Expand Up @@ -1723,6 +1884,9 @@ def _export_with_scalebar(exportim,pixelsize,unit,filename,multichannel,
in zip(shape,crop[:2])] + list(crop[2:])
altcrop = True
x,y,w,h = crp
if crop_unit == 'data':
w = w/pixelsize
h = h/pixelsize
else:
crp = [[cc if cc>0 else s+cc for cc in c]\
for s,c in zip(shape,crop)]
Expand All @@ -1736,13 +1900,18 @@ def _on_lim_change(call):
xmin,xmax = ax.get_xlim()
ymax,ymin = ax.get_ylim()
if altcrop:
croptext = 'current crop: ({:}, {:}, {:}, {:})'
croptext = croptext.format(
int(xmin),
int(ymin),
int(xmax-xmin+1),
int(ymax-ymin+1)
)
if crop_unit == 'data':
croptext = 'current crop: ({:}, {:}, {:.4g} {}, {:.4g} {})'
croptext = croptext.format(
int(xmin),
int(ymin),
pixelsize*(xmax-xmin+1),unit,
pixelsize*(ymax-ymin+1),unit
)
else:
croptext = 'current crop: ({:}, {:}, {:}, {:})'
croptext = croptext.format(
int(xmin),int(ymin),int(xmax-xmin+1),int(ymax-ymin+1))
else:
croptext = 'current crop: (({:}, {:}), ({:}, {:}))'
croptext = croptext.format(
Expand All @@ -1768,7 +1937,17 @@ def _on_lim_change(call):

#if (x,y,w,h) format, convert to other format
if len(crop) == 4:
crop = ((crop[0],crop[1]),(crop[0]+crop[2],crop[1]+crop[3]))
if crop_unit == 'pixels':#w and h specified in pixels
crop = ((crop[0],crop[1]),(crop[0]+crop[2],crop[1]+crop[3]))
elif crop_unit == 'data':#w and h specified in data units
crop = ((crop[0],crop[1]),(
int(round(crop[0]+crop[2]/pixelsize)),
int(round(crop[1]+crop[3]/pixelsize))
))
else:
raise ValueError('`crop` must be "pixels" or "data"')
elif crop_unit == 'data':
warn('`crop_unit="data"` is only implemented for (x,y,w,h) format')

#crop and update shape
if multichannel:
Expand Down
18 changes: 18 additions & 0 deletions scm_confocal/visitech.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -592,6 +592,15 @@ def export_with_scalebar(self,frame=0,filename=None,**kwargs):
optional rescaling using `resolution`).
The default is `None` which takes the entire image.
crop_unit : `'pixels'` or `'data'`, optional
sets the unit in which the width and height in `crop` are
specified when using the (x,y,w,h) format, with `'pixels'` to give
the size in pixels or `'data'` to specify the size in the physical
unit used for the scalebar (after optional unit conversion via the
`convert` parameter). Note that the position of the top left corner
is given in pixels. The `((xmin,ymin),(xmax,ymax))` format must be
always given in pixels, and `crop_unit` is ignored if `crop` is
given in this format. The default is `'pixels'`.
resolution : int, optional
the resolution along the x-axis (i.e. image width in pixels) to use
for the exported image. The default is `None`, which uses the size
Expand Down Expand Up @@ -1452,6 +1461,15 @@ def export_with_scalebar(self,stack=0,zslice=0,filename=None,**kwargs):
optional rescaling using `resolution`).
The default is `None` which takes the entire image.
crop_unit : `'pixels'` or `'data'`, optional
sets the unit in which the width and height in `crop` are
specified when using the (x,y,w,h) format, with `'pixels'` to give
the size in pixels or `'data'` to specify the size in the physical
unit used for the scalebar (after optional unit conversion via the
`convert` parameter). Note that the position of the top left corner
is given in pixels. The `((xmin,ymin),(xmax,ymax))` format must be
always given in pixels, and `crop_unit` is ignored if `crop` is
given in this format. The default is `'pixels'`.
resolution : int, optional
the resolution along the x-axis (i.e. image width in pixels) to use
for the exported image. The default is `None`, which uses the size
Expand Down

0 comments on commit 7058b65

Please sign in to comment.