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Bug when saving to vector format (pdf, svg, eps) #2831
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That is bad. This is maybe related to #2889 ?
Can confirm this on master.
If you set the dpi to 100 it more-or-less works correctly, you can see the corners of the red sequare outside of the edges of the annotation box, but it is in the right place.
P.S. A screenshot of the problem:
So the red box is in the wrong place for the plot.
Interestingly, if you don't specify the correct DPI at savefig for PNG, the red box is also in the wrong place. Something is a little fishy there...
@pelson The similarity is (I think) related to using get_extent in one context which creates values based on current screen-space transforms. The values are then saved and get re-used with different screen-space transforms which causes things to be the wrong size/in the wrong place.
The similarity is (I think) related to using get_extent in one context which creates values based on current screen-space transforms.
Agreed. The issue can be seen with all backends with a simple modification to @wronk 's code:
import numpy as np import matplotlib.pyplot as plt from matplotlib.image import BboxImage bboxProp = dict(boxstyle='round,pad=0.3', fill=False, ec='red', linewidth=8) ax = plt.axes() midBox3 = ax.annotate(r'$j_{N-1}$', xy=(0, .5), xycoords='axes fraction', xytext=(0.7, 0.7), textcoords='axes fraction', size=50, ha='left', va='center', bbox=bboxProp, arrowprops=None, color='black') ax.add_artist(BboxImage(midBox3.get_bbox_patch().get_window_extent, data=np.zeros_like(np.atleast_2d(np.arange(256)/256.)))) ax.set_ylim(bottom=-1) plt.show()The key is that the red box only appears after the figure has been re-drawn. The change in x/y limit is significant here.
@pelson @efiring @mdboom I am going to punt this and the related issues to 1.5 (at least).
My understanding of the problem here is that artists are being lined up in screen-space (through get_window_extent) and then when things get updated underneath the artists the changes don't propagate. I think any fix for this will be a major overhaul.
I will create an issue to add a note to get_window_extent docs warning that it can lead to this sort of thing.
@tacaswell - do you know if #3054 fixes this issue?
I don't, but should probably check (I left this comment before I found that patch).
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This "fixes" the problem
...: if saveFig: ...: pdfFile = PdfPages(save_fname + 'flowchart_PDF.pdf') ...: plt.savefig(BytesIO(), format='pdf', dpi=fig.dpi) ...: plt.savefig(pdfFile, format='pdf', dpi=fig.dpi) ...: pdfFile.close() ...: plt.savefig(save_fname + 'flowchart_PNG.png', dpi=fig.dpi) ...: plt.show()
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Re-evaluating this, I think @leejjoon is completely correct. The source of the problem is that for zorder reasons we have to draw the background before the text, but the text does not know how big it is before has been drawn.
Short of implementing a system to automatically detect when we need to render multiple times there are two fixes:
- do a manually "dummy" save to a BytesIO with the exact same settings as you want to save the output as.
- use layuot='constrained' or layout='tight' which internally do a dummy render to get all the text sizes so that they can then update the layout.
- added a commit that references this issue on Apr 13, 2025
- added a commit that references this issue on Apr 13, 2025
1. do a manually "dummy" save to a `BytesIO` with the exact same settings as you want to save the output as.
Does this work? I believe not reliably just with a savefig, because it only replaces the canvas temporarily.
If I do:
In [6]: print(ax.transData) CompositeGenericTransform( [...] BboxTransformTo( TransformedBbox( Bbox(x0=0.125, y0=0.10999999999999999, x1=0.9, y1=0.88), BboxTransformTo( TransformedBbox( Bbox(x0=0.0, y0=0.0, x1=6.4, y1=4.8), Affine2D().scale(100.0))))))) In [7]: fig.savefig('test.png', dpi=50) In [8]: print(ax.transData) CompositeGenericTransform( [...] BboxTransformTo( TransformedBbox( Bbox(x0=0.125, y0=0.10999999999999999, x1=0.9, y1=0.88), BboxTransformTo( TransformedBbox( Bbox(x0=0.0, y0=0.0, x1=6.4, y1=4.8), Affine2D().scale(100.0)))))))the Affine2D().scale(100.0) is the dpi scaling so I won't get my dpi=50 into the window extent ?!?
Another approach would be to use a callable object that explicitly update the position of the text and the patch. This does not require rendering the figure twice
def get_bbox(renderer): midBox3.update_positions(renderer) midBox3.update_bbox_position_size(renderer) return midBox3.get_bbox_patch().get_window_extent(renderer) arr = np.atleast_2d(np.arange(256)/256.) bbox_image = BboxImage(get_bbox, data=arr) ax.add_artist(bbox_image)
Yet another option is to use patheffects. The example code below uses mpl_visual_context module which I created.
from matplotlib.patheffects import Normal from mpl_visual_context.patheffects import FillImage bbox_image = BboxImage(midBox4.get_bbox_patch().get_window_extent, data=arr) midBox3.get_bbox_patch().set_path_effects([FillImage(bbox_image, ax=ax), Normal()])
Does this work?
My understanding is that in similar cases (passing arg.get_window_extent as a callable referring to something later in the draw order, that artist may move/resize itself as part of the draw, and saving to a vector format) this will work reliably. Because vector backends always set the dpi to 72 (because we need all of the "screen" positions that come out to be in inches) so doing draw_without_render without doing the same won't work. The fist save will get the wrong position for the box, correct the position of the text which is preserved in some state (I'm not entirely sure which state) between draws so in the second draw the box is in the right place and the text recomputes to the same place.
@leejjoon's suggestion will work 100% with only one save, but requires the user to know which methods to call to update the correct state.
There is a discrepancy between vector format (pdf, svg, eps) output and image output (png, jpg, etc) for the BboxImage object. I can't attach a pdf, but the this code creates and saves a pdf and png illustrating the BboxImage object translation. Just update the save folder path to run the code.
Thanks and let me know if I should include anything else.
''' Minimum working example version 1.3.1 Plots a descriptive flowchart showing error @Author: wronk ''' from os import path as op import numpy as np import matplotlib as mpl import matplotlib.pyplot as plt from matplotlib.image import BboxImage from matplotlib.offsetbox import TextArea, AnnotationBbox from matplotlib.transforms import Bbox from mpl_toolkits.axes_grid1 import make_axes_locatable from matplotlib.backends.backend_pdf import PdfPages ############################################################################### #EDIT SAVE FOLDER TO AUTOSAVE saveFig = True save_fname = '/home/wronk/' mpl.rcParams['mathtext.default'] = 'rm' #Box properties bboxProp = dict(boxstyle='round,pad=0.3', fill=False, ec='w', linewidth=8) #Colors for annotation arrows senCol = (0.35, 0.35, 0.35) srcCol = (.8, .216, 0.0) #Define color map cm = 'autumn' colRange = np.atleast_2d(np.arange(256)/256.) ############################################################################### #Initialize Plot plt.ion() plt.close('all') mpl.rcParams['pdf.fonttype'] = 42 figSize = (12, 6) ftSize = 32 dpi = 80 rowYVals = [0.085, 0.55, 0.85] rowXVals = [0, .075, .2, .34, .5, .65, .8, .875] fig = plt.figure(figsize=figSize, facecolor='white', dpi=dpi) #fig = plt.figure(figsize=figSize, facecolor='white') #ax = fig.gca() ax = plt.subplot(111) ############################################################################### #Mid level of annotation boxes #Text for boxes in mathematical font flowMid = r'$j_{N-1}$' midBox3 = ax.annotate(flowMid, xy=(0, .5), xycoords='axes fraction', xytext=(rowXVals[3], rowYVals[1]), textcoords='axes fraction', size=ftSize, ha='left', va='center', bbox=bboxProp, arrowprops=None, color='black') ####################################### #HEREIN LIES THE PROBLEM #Add color (gradients) behind the boxes #Something about the bbox window extent property must get shifted when saving #as a vector format (pdf, svg, eps) but not common image types. In my experience, #every bboximage was translated and scaled uniformly. #I tried changing DPI, image size, subplot parameters as well as sychronizing #plotting and saving figures in matplotlibrc to no avail. DPI does seem to #have some sort of effect in terms of how the bboximage gets shifted though. gradient = BboxImage(midBox3.get_bbox_patch().get_window_extent, data=np.zeros_like(colRange), cmap=cm, norm=None, origin=None) ax.add_artist(gradient) ####################################### plt.draw() #Save figure as pdf and png to highlight difference #Same results when saving from GUI window if saveFig: pdfFile = PdfPages(save_fname + 'flowchart_PDF.pdf') plt.savefig(pdfFile, format='pdf', dpi=fig.dpi) pdfFile.close() plt.savefig(save_fname + 'flowchart_PNG.png', dpi=fig.dpi) plt.show()(tacaswell edited for code markup)