How can I get matplotlib plots as emf or wmf files that are usable as vector graphics in MS Office (Word and PowerPoint)?
I've tried exporting to svg and converting to emf using both Inkscape and LibreOffice Draw, but both of those options seem to cause image quality loss resulting in raster images.
I've also tried exporting to pdf and converting to emf/wmf, but that has the same issue.
To save figures as .emf file in matplotlib using Linux, try the following:
Install Inkscape (I have installed Inkscape 0.92.4 in Ubuntu 16.04. Other versions should work alike)
In matplotlib, save the figure as .svg and then convert it to .emf via an Inkscape subprocess call.
For example:
import numpy as np
import subprocess
import matplotlib.pyplot as plt
x = np.arange(2,50,step=2)
y = x**2
plt.plot(x,y)
plt.savefig('y_is_x^2.svg', format='svg', bbox_inches='tight')
subprocess.call('inkscape y_is_x^2.svg -M y_is_x^2.emf',shell=True)
You can then insert the .emf figure as a picture in MS Word or PowerPoint. The quality is near .svg. Be warned though, large .svg files may not work.
Here is my solution to create WMF and SVG. You can install Inkscape and use the following class, 'SaveAndClosePlot' creates SVG and then by using the Inkscape it converted to WMF. TestPlot function can be customized for your need.
import os
from pathlib import Path
from ConfigParserM import logging
import subprocess
from matplotlib import pyplot as plt
class SVG_WMF_Plot:
def __init__(self):
self.__folderNameGraph = 'Graphs'
self.__WMF_SVGSaving = True
self.__inkScapePath = "C://Program Files//inkscape//inkscape.exe"
self.__figureDPI = 500
def getRootDirectory(self):
try:
return Path(os.path.dirname(os.path.realpath('__file__')))
except Exception as e:
logging.exception(e)
raise
def getAddressTo(self, Main=None, FolderName=None, FileName=None, Extension=None):
try:
if Main is None:
Main = self.getRootDirectory()
if FolderName:
Path1 = Path(Main) / Path(FolderName)
else:
Path1 = Path(Main)
if not os.path.exists(Path1):
os.makedirs(Path1)
if FileName:
if Extension:
File_Address = Path1 / Path(FileName + "." + Extension)
else:
File_Address = Path1 / Path(FileName)
else:
File_Address = Path1
return File_Address
except Exception as e:
logging.exception(e)
raise
def TestPlot(self):
try:
fig, ax1 = plt.subplots()
x = [1, 2]
y = [1, 2]
F1 = 'test'
ax1.plot(x, y)
self.SaveAndClosePlot(folderName=self.__folderNameGraph, fileName=F1)
except Exception as e:
logging.exception(e)
raise
def SaveAndClosePlot(self, folderName, fileName):
try:
Address = self.getAddressTo(FolderName=self.__folderNameGraph + f"\{folderName}", FileName=fileName, Extension="jpg")
plt.savefig(Address, format='jpg', dpi=self.__figureDPI, bbox_inches='tight')
if self.__WMF_SVGSaving:
Address = self.getAddressTo(FolderName=self.__folderNameGraph + f"\{folderName}", FileName=fileName, Extension="svg")
plt.savefig(Address, format='svg', dpi=self.__figureDPI, bbox_inches='tight')
# add removing SVG if needed
AddressWMF = self.getAddressTo(FolderName=self.__folderNameGraph + f"\{folderName}", FileName=fileName, Extension="wmf")
subprocess.call([self.__inkScapePath, str(Address.resolve()), '--export-wmf', str(AddressWMF.resolve())])
plt.clf()
plt.close()
except Exception as e:
logging.exception(e)
raise
Related
I have read that you can use a bytes like object to reportlab.lib.utils.ImageReader(). If I read in a file path it works fine, but I want to use a byte like object instead that way I can save the plot I want in memory, and not have to constantly be saving updated plots on the drive.
This is where I found the code to convert the image into a string
https://www.programcreek.com/2013/09/convert-image-to-string-in-python/
This is an example of how to use BytesIO as input for ImageReader()
How to draw image from raw bytes using ReportLab?
This class is used to make a plot and pass in a save it to memory with BytesIO(). string is the value I'm going to pass later
#imports
import PyPDF2
from io import BytesIO
from reportlab.lib import utils
from reportlab.lib.pagesizes import landscape, letter
from reportlab.platypus import (Image, SimpleDocTemplate,
Paragraph, Spacer)
from reportlab.lib.styles import getSampleStyleSheet
from reportlab.lib.units import inch, mm
import datetime
import os
import csv
import io
import base64
import urllib
from django.contrib import admin
from django.forms import model_to_dict
from django.http import HttpResponse
from django.urls import path
from django.views.decorators.csrf import csrf_protect
from django.utils.decorators import method_decorator
from reporting import models, functions, functions2
import matplotlib
matplotlib.use('agg')
from matplotlib import pyplot as plt
import numpy as np
def make_plot(data):
items = [tuple(item) for item in data.items()]
keys = [item[0] for item in items]
vals = [item[1] for item in items]
fig, ax = plt.subplots()
ind = np.arange(len(keys)) # the x locations for the groups
width = 0.35 # the width of the bars
rects1 = ax.bar(ind - width/2, vals, width)
ax.set_ylabel('Count')
ax.set_xticks(ind)
ax.set_xticklabels(keys)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
string = base64.b64encode(buf.read())
return 'data:image/png;base64,' + urllib.parse.quote(string), string
This is the minimum code to show how the information is moved to where the error occurs.
class ProgressReportAdmin(ReadOnlyAdmin):
current_extra_context = None
#csrf_protect_m
def changelist_view(self, request, extra_context=None):
plot = make_plot(data)
self.current_extra_context = plot[1]
def export(self, request):
image = self.current_extra_context
pdf = functions.LandscapeMaker(image, fname, rotate=True)
pdf.save()
This is where the error occurs, in the scaleImage function
class LandscapeMaker(object):
def __init__(self, image_path, filename, rotate=False):
self.pdf_file = os.path.join('.', 'media', filename)
self.logo_path = image_path
self.story = [Spacer(0, 1*inch)]
def save(self):
fileObj = BytesIO()
self.doc = SimpleDocTemplate(fileObj, pagesize=letter,
leftMargin=1*inch)
self.doc.build(self.story,
onFirstPage=self.create_pdf)
def create_pdf(self, canvas, doc):
logo = self.scaleImage(self.logo_path)
def scaleImage(self, img_path, maxSize=None):
#Error1 occurs on
img = utils.ImageReader(img_path)
img.fp.close()
#Error2
#image = BytesIO(img_path)
#img = utils.ImageReader(image)
#img.fp.close()
For Error1 I receive:
raise IOError('Cannot open resource "%s"' % name)
img = utils.ImageReader(img_path)
"OSError: Cannot open resource "b'iVBORw0KGgoAAA' etc.,
For Error2 I receive
OSError: cannot identify image file <_io.BytesIO object at 0x7f8e4057bc50>
cannot identify image file <_io.BytesIO object at 0x7f8e4057bc50>
fileName=<_io.BytesIO object at 0x7f8e4057bc50> identity=[ImageReader#0x7f8e43fd15c0]
I think you have to pass buff to ImageReader somehow.
I'm using this function to save and draw the figures I generate with matplotlib and it works perfectly for me.
seek(offset, whence=SEEK_SET) Change the stream position to the given offset. Behaviour depends on the whence parameter. The default value for whence is SEEK_SET.
getvalue() doesn't work except the seek(0)
def save_and_draw(fig, x_img, y_img, width_img=width_img, height_img=height_img):
imgdata = BytesIO()
fig.savefig(imgdata, format='png')
imgdata.seek(0)
imgdata = ImageReader(imgdata)
self.c.drawImage(imgdata, x_img, y_img, width_img, height_img)
plt.close(fig)
I'm new to the world of python. I'm trying to create a plot showing accumulated GDD (Growing degree days) vs time for selected cities within a given period of time
I wrote a function to accomplish this, but I can't seem to get it to work right. I keep getting with an empty plot in it. Also a dimension error. Anyone know how i can solve these issues.
Any help/suggestions is appreciated!
Here is the code
import sys, argparse, csv
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import datetime as dt
def open_file(file_name, mode):
"""Open a file."""
try:
with open(sys.argv[1], 'r') as the_file:
filename=the_file.read()
except IOError as err:
print("Unable to open the file", file_name, "Ending program.\n", err)
input("\n\nPress the enter key to exit.")
sys.exit()
else:
return filename
"""Cities.txt file as an argument"""
try:
my_file = open_file(sys.argv[1], 'r')
except:
print("GDD needs one argument", "\nEnding program...\n")
input("Press the enter key to exit.")
sys.exit()
extension=".csv"
for line in my_file.splitlines():
file_name=line+extension
print(file_name)
with open('data/'+ file_name, "rU") as files:
val = list(csv.DictReader(files))
l = []
for i in range(0, len(val)):
row = val[i]
if row['Min Temp'] == '' or row['Max Temp'] == '':
pass
else:
GDD = ((float(row['Min Temp']) + float(row['Max Temp']))/2)-10
l.append(GDD)
val[i]['GDD'] = GDD
#print(row['Min Temp'], ' ' , row['Max Temp'], ' ', str(round(row['GDD'], 2)))
#plt.subplot(1,1,1)
#x = np.linspace(1, 12, 365, endpoint=True)
x = np.linspace(1, 12, 365, endpoint=True)
plt.plot(x,GDD, label = file_name.split(',')[0])
plt.gcf().autofmt_xdate()
plt.legend(loc="upper left")
plt.xlabel('Months', color='black')
plt.ylabel('Cumulative GDD (>10°C)')
plt.title('Accumulated Growing Degree Days')
plt.draw()
A simple and fast solution could be to add plt.hold(True) after a plot call.
A more clean solution is to use a figure which can bee seen as window which you draw onto. just like in this example
So you'd define a figure, keep its reference, add axes and perform all action on these axes
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.4, 0.7])
ax.plot(...)
I am using the following Python script:
import numpy as np
import matplotlib.pyplot as plt
import nibabel
import os
def collapse_probtrack_results(waytotal_file, matrix_file):
with open(waytotal_file) as f:
waytotal = int(f.read())
data = nibabel.load(matrix_file).get_data()
collapsed = data.sum(axis=0) / waytotal * 100.
return collapsed
matrix_template = 'results/{roi}.nii.gz.probtrackx2/matrix_seeds_to_all_targets.nii.gz'
processed_seed_list = [s.replace('.nii.gz','').replace('label/', '')
for s in open('/home/salvatore/tirocinio/aal_rois_diff_space/aal.txt').read().split('\n')
if s]
N = len(processed_seed_list)
conn = np.zeros((N, N))
rois=[]
idx = 0
for roi in processed_seed_list:
matrix_file = template.format(roi=roi)
seed_directory = os.path.dirname(result)
roi = os.path.basename(seed_directory).replace('.nii.gz.probtrackx2', '')
waytotal_file = os.path.join(seed_directory, 'waytotal')
rois.append(roi)
try:
# if this particular seed hasn't finished processing, you can still
# build the matrix by catching OSErrors that pop up from trying
# to open the non-existent files
conn[idx, :] = collapse_probtrack_results(waytotal_file, matrix_file)
except OSError:
pass
idx += 1
# figure plotting
fig = plt.figure()
ax = fig.add_subplot(111)
cax = ax.matshow(conn, interpolation='nearest', )
cax.set_cmap('hot')
caxes = cax.get_axes()
When I try to run it I get the following error: NameError: name 'template' is not defined. This refers to line 22 of the script above. Can you please help me to figure out what is this about?
There is no variable like template, so template cannot be used in the right side of the expression. Try
matrix_file = matrix_template.format(roi=roi)
instead.
This is related to another question I posted, but is more specific (and hopefully gets more specific answers).
I am trying to display png images on an IPython notebook, and update the display as the png files are updated.
One possible solution is below. Unfortunately, my implementation does not update the file, and creates a new HTML block at the end of the old one. What I want instead, is to replace the old HTML block with the new one -i.e. replace the content only.
As example code, I have two notebooks. One notebook generates pngs and saves them in a figures directory.
import os
import glob
import time
import matplotlib.pyplot as plt
import numpy as np
for ix in range(20):
N = 50
x = np.random.rand(N)
y = np.random.rand(N)
colors = np.random.rand(N)
area = np.pi * (15 * np.random.rand(N))**2 # 0 to 15 point radiuses
fig = plt.figure(figsize=(8,8))
plt.scatter(x, y, s=area, c=colors, alpha=0.5)
fig.savefig(os.path.join("figures", "fig1.png"), bbox_inches="tight")
plt.close(fig)
time.sleep(3)
A second notebook shows the pngs It is supposed top show a single png which updates. Instead it stacks the same png on itself, every time the png is updated.
import os
import time
from IPython.html.widgets import interact, interactive, fixed
from IPython.html import widgets
from IPython.display import clear_output, display, HTML
def get_latest_file_ts(directory="figures", file_name="fig1.png", strip_directory=True):
"""
Continuously check for modifications to the file file_name in directory. If file has been
modified after touched_on, return the Unix timestamp of the modification time.
:param directory: string / the directory where the file is
:param file_name: string / the file name
:param strip_directory: boolean / if True, strip the directory part of the file name
:return:
"""
if strip_directory:
fname = os.path.join(directory, file_name)
else:
fname = file_name
try:
return os.stat(fname).st_mtime
except:
print "FileNotFoundException: Could not find file %s" % fname
return None
def check_if_modified_file(directory="figures", file_name="fig1.png",
touched_on=1420070400, sleep_time=1, strip_directory=True):
"""
Continuously check for modifications to the file file_name in directory. If file has been
modified after touched_on, return the Unix timestamp of the modification time.
:param directory: string / the directory where the file is
:param file_name: string / the file name
:param touched_on: float / the Unix timestamp on which the file was last modified
:param sleep_time: float / wait time between interactions
:param strip_directory: boolean / if True, strip the directory part of the file name
:return:
"""
if strip_directory:
fname = os.path.join(directory, file_name)
else:
fname = file_name
while True:
try:
latest_touch = os.stat(fname).st_mtime
if latest_touch == touched_on:
time.sleep(sleep_time)
else:
return latest_touch
except:
print "FileNotFoundException: Could not find %s" % fname
return None
def show_figs(directory="figures", file_name="fig1.png"):
s = """<figure>\n\t<img src="%s" alt="The figure" width="304" height="228">\n</figure>""" % os.path.join(directory, file_name)
display(HTML(s))
timestamp = get_latest_file_ts(directory="figures", file_name="fig1.png", strip_directory=True)
show_figs(directory="figures", file_name="fig1.png")
cnt = 1
while True and cnt < 4:
timestamp = check_if_modified_file(directory="figures", file_name="fig1.png", touched_on=timestamp, sleep_time=1, strip_directory=True)
display(HTML(""))
show_figs(directory="figures", file_name="fig1.png")
time.sleep(1)
cnt += 1
(as you can see I have added upper limits on the executions of both the generator and consumer loops)
Any help on how to make widgets update HTML content would be awesome.
The problem that you only see the first image is very likely related to caching of the browser. To overcome this issue a simple solution is to add a varying query string to the image src as shown e.g. here.
Thus your show_figs method could look like:
import time
def show_figs(directory="figures", file_name="fig1.png"):
s = """<figure>\n\t<img src="{0}?{1}" alt="The figure" width="304" height="228">\n</figure>""".format(os.path.join(directory, file_name),time.time())
display(HTML(s))
In combination with the clear_output function you should be able to get your updated image.
Im using python 3.4 and Django 1.8. I want to "print" a matplotlib result in a Django template. I reach this a few days ago, so I continue in other things of my Django App. Now, I dont know why, I was going to show the result to a friend, and my template with a matplotlib graph, now shows a big code! I dont know why this happen, because my view doesnt change in anything from when it was showing the right graph! Please help me!
This is my view!
from django.shortcuts import render
from matplotlib import pylab
from pylab import *
import PIL
import PIL.Image
import io
from io import *
def graphic(request):
pos = arange(10)+ 2
barh(pos,(1,2,3,4,5,6,7,8,9,10),align = 'center')
yticks(pos,('#hcsm','#ukmedlibs','#ImmunoChat','#HCLDR','#ICTD2015','#hpmglobal','#BRCA','#BCSM','#BTSM','#OTalk'))
xlabel('Popularity')
ylabel('Hashtags')
title('Hashtags')
subplots_adjust(left=0.21)
buffer = io.BytesIO()
canvas = pylab.get_current_fig_manager().canvas
canvas.draw()
graphIMG = PIL.Image.fromstring('RGB', canvas.get_width_height(), canvas.tostring_rgb())
graphIMG.save(buffer, "PNG")
content_type="Image/png"
buffercontent=buffer.getvalue()
graphic = (buffercontent ,content_type)
pylab.close()
return render(request, 'graphic.html',{'graphic':graphic})
Of course in my graphic.html is a variable called {{graphic}} inside a blockcontent!
This was showing the right result in my template! What happen?
Now sometimes when i run my template it shows a big code, or just show me this django error:
Exception Value:
main thread is not in main loop
Exception Location: C:\Python34\lib\site-packages\matplotlib\backends\tkagg.py in blit, line 17
Help!
from io import BytesIO
import base64
import matplotlib.pyplot as plt
import numpy as np
def graphic(request):
pos = np.arange(10)+ 2
fig = plt.figure(figsize=(8, 3))
ax = fig.add_subplot(111)
ax.barh(pos, np.arange(1, 11), align='center')
ax.set_yticks(pos)
ax.set_yticklabels(('#hcsm',
'#ukmedlibs',
'#ImmunoChat',
'#HCLDR',
'#ICTD2015',
'#hpmglobal',
'#BRCA',
'#BCSM',
'#BTSM',
'#OTalk',),
fontsize=15)
ax.set_xticks([])
ax.invert_yaxis()
ax.set_xlabel('Popularity')
ax.set_ylabel('Hashtags')
ax.set_title('Hashtags')
plt.tight_layout()
buffer = BytesIO()
plt.savefig(buffer, format='png')
buffer.seek(0)
image_png = buffer.getvalue()
buffer.close()
graphic = base64.b64encode(image_png)
graphic = graphic.decode('utf-8')
return render(request, 'graphic.html',{'graphic':graphic})
and in the template:
<img src="data:image/png;base64,{{ graphic|safe }}">
I have:
matplotlib==3.0.2 and Django==2.1.4
Edit:
try with
graphic = cStringIO.StringIO()
canvas.print_png(graphic)
return render(request, 'graphic.html',{'graphic':graphic})
You have to specify that your image is a binary string:
<img src="data:image/png;base64,{{graphic|safe}}">
Or actually save it to the filesystem and provide the path.
Alternatively you could use Bokeh which can give you the html + javascript to embed the plot directly in the template, then it is dynamically generated and brings nice features.
The final solution was to create a special view that returns the matplotlib plot in an empty template, like this:
def grafico (rquest):
pos = arange(10)+ 2
barh(pos,(1,2,3,4,5,6,7,8,9,10),align = 'center')
yticks(pos,('#hcsm','#ukmedlibs','#ImmunoChat','#HCLDR','#ICTD2015','#hpmglobal','#BRCA','#BCSM','#BTSM','#OTalk'))
xlabel('Popularidad')
ylabel('Hashtags')
title('Gráfico de Hashtags')
subplots_adjust(left=0.21)
buffer = io.BytesIO()
canvas = pylab.get_current_fig_manager().canvas
canvas.draw()
graphIMG = PIL.Image.fromstring('RGB', canvas.get_width_height(), canvas.tostring_rgb())
graphIMG.save(buffer, "PNG")
pylab.close()
return HttpResponse (buffer.getvalue(), content_type="Image/png")
The next step is to put in your template this:
<img src="url_of_the_graphic_view">
And thats all!
def show(request):
x = np.arange(10)
y = x
fig = plt.figure()
plt.plot(x, y)
canvas = fig.canvas
buf, size = canvas.print_to_buffer()
image = Image.frombuffer('RGBA', size, buf, 'raw', 'RGBA', 0, 1)
buffer=io.BytesIO()
image.save(buffer,'PNG')
graphic = buffer.getvalue()
graphic = base64.b64encode(graphic)
buffer.close()
return render(request, 'graphic.html',{'graphic':graphic})
I had a broken icon image as well, after using the answers above, and I fixed it by removing the b' and ' from the graphic base64 binary representation :
return render(request, 'graphic.html', {'graphic': str(graphic)[2:-1]})