I have a piece of code that draws text on top of an image in my Rails app and since short while ago, probably having to to with upgrading to OS X Yosemite, it's having an issue with reading fonts on my local machine (production server is working fine).
I can reduce it to this example:
require 'rvg/rvg'
font = '"/Users/xxxxxxxx/xxxx/app/assets/fonts/PTSans-Regular.ttf"'
rvg = Magick::RVG.new(100,100) do |canvas|
canvas.text(0, 0, 'my text').styles(font: font)
end
rvg.draw
I get this error
Magick::ImageMagickError: unable to read font `"/Users/xxxxxxxx/xxxx/app/assets/fonts/PTSans-Regular.ttf"' # error/annotate.c/RenderFreetype/1153: `(null)'
from /Users/xxxxxxxx/.rvm/gems/ruby-2.0.0-p353#xxxxxxxx/gems/rmagick-2.13.2/lib/rvg/misc.rb:322:in `get_type_metrics'
I tried reinstalling imagemagick and the rmagick gem, also with these flags:
brew install imagemagick --disable-openmp --build-from-source
Also, if I change
font = "/Users/xxxxxx/xxxxx/app/assets/fonts/PTSans-Regular.ttf"
thinking that the extra quotes could get in the way, then I get
Magick::ImageMagickError: non-conforming drawing primitive definition `Users/xxxxx/xxxx/app/assets/fonts/PTSans-Regular.ttf' # error/draw.c/DrawImage/3170
from /Users/xxxxxxx/.rvm/gems/ruby-2.0.0-p353#xxxx/gems/rmagick-2.13.2/lib/rvg/misc.rb:546:in `draw'
I have also tried to install the latest version of XQuartz from http://xquartz.macosforge.org/landing/
Strangely enough, this fixed it:
brew install gs
The error got me confused because it didn't say anything about ghostscript, however, it worked according to https://stackoverflow.com/a/13936374/322253
Related
When i use pydicom in python3.6, there are some problem:
import pydicom
import matplotlib.pyplot as plt
import os
import pylab
filePath = "/Users/zhuangrui/Documents/Python/Dicom/dicoms/zhang_bo/0001.dcm"
dataSet_1 = pydicom.dcmread(filePath)
plt.imshow(dataSet_1.pixel_array)
plt.show()
here is the problem:
How can this problem be solved？ Thank you very much！
I've faced with the same problem, after doing some research on the suggested link above. I've managed to solve it by updating to the latest pydicom module "1.2.0" and installing gdcm. You can update the pydicom with
pip install -U git+https://github.com/pydicom/pydicom.git
You can find the latest gdcm here and this link explains the installation.
I use anaconda and it's easier to install the gdcm package and solve the problem. If you use anaconda
just type inside from your environment:
conda install pydicom --channel conda-forge to get pydicom's latest and
conda install -c conda-forge gdcm
to get the gdcm. This resolves the problem. Hope these will help.
With pydicom, you need an appropriate image handler also installed to handle compressed image types.
For JPEG lossless, in theory the following should work: jpeg_ls, gdcm, or Pillow with jpeg plugin. All of these also require Numpy to be installed. See the discussion at https://github.com/pydicom/pydicom/issues/532.
There is also a pull request in progress to add more descriptive error messages for what image handlers are needed for different images.
Problem:
I was trying to read medical images with .dcm extension. But was getting an error on Windows as well as on Ubuntu. I find a solution which will work on both the machined.
The error I got on Ubuntu is: NotImplementedError: this transfer syntax JPEG 2000 Image Compression (Lossless Only), can not be read because Pillow lacks the jpeg 2000 decoder plugin
(Note for Windows I was getting a different error but I am sure it's because of the same issue i.e. Pillow does not support JPEG 2000 format)
Platforma Information:
I am using: Python 3.6, Anaconda and Ubuntu, 15 GB RAM
RAM is important:
The solution I applied is the same as Ali explained above. But I want to add this installation may take time (depending on RAM you are using). On ubuntu where I am using 15 GB RAM on Cloud platform taken less time and on Windows on a local machine having 4 GB RAM taken a lot of time.
Solution
Anaconda is necessary. Why?
Please check the official doc of pydicom (https://pydicom.github.io/pydicom/dev/getting_started.html) its mentioned "To install pydicom along with image handlers for compressed pixel data, we encourage you to use Miniconda or Anaconda" (Note for Windows I was getting a different error)
If you are using Ubuntu directly open Terminal. If you are using Windows then on Anaconda Navigator go to Environment from here start terminal. Execute the following commands on it:
pip install -U git+https://github.com/pydicom/pydicom.git
conda install pydicom --channel conda-forge
conda install -c conda-forge gdcm
Cross Check:
Now use .dcm file for which we got the Error. Try to use the following code in Python notebook
filename = 'FileName.dcm'
ds = pydicom.dcmread(filename)
plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
It should print the output. Also try this code:
ds.pixel_array
This will give you the array containing values.
Hello stack community!
I'm not sure if my question is graph-tool related or gtk-related, but maybe both. Moreover, sorry if what I did while trying to solve it is plain stupid, I'm not a programmer by formal education, so I know just as much as I could find by google and comprehend.
Here is the problem:
After I brew install graph-tool, launch python and try to import graph_tool.all I get the following error:
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.py:1318: RuntimeWarning: Error importing Gtk module: No module named repository; GTK+ drawing will not work.
Previously I was sure that if import pygtk; pygtk.require('2.0'); import gtk works, that means the error is a graph-tool issue, but that don't have to be the case since graph-tool might use gtk (3??) and GObject (right?) and the upper checks for gtk2 and pygtk ( This question led me to this thought ).
I tried reinstalling gtk, GObject and all dependencies. Wipe all brew-related and brew itself and then reinstall everything (as in here). Still same error appears. I also tried to unlink everything from brew and link it again just to be sure, but this does not change anything either.
What else did I check:
I'm running MAC OS X Version 10.10.3, homebrew-installed python 2.7.10 (python --version returns Python 2.7.10 which is the one installed by brew; which python points to /usr/local/bin/python). brew info graph-tool shows that all requirements of it are there (even the optional ones). GTK 2.24.28, GTK+3 3.16.4, PyGobject 2.28.6, GObject-introspection 2.28.6, Cairo 1.14.2, Py2Cairo 1.10.0, pango 1.36.8, XQuartz 2.7.7 etc are installed, dependencies of those are fine as well. gi 1.2 is installed (via pip), gi.repository is indeed not there. I am aware of this question, but I have PyGObjects installed.
I also read this question and the reply, but none of this solves my problem as far as I can judge.
I've spend two days looking for the solution, so any help is appreciated.
It's seem to be a cairo dependency issue.
As you may see here, graph-tool package require a lot of depencies (numpy, gfortran, scipy, freetype, libpng, matplotlib, boost, cgal, graphviz, cairo, cairomm, py2cairo)
In your case you may probably solve the issue with a clean reinstall of "cairo".
Try those commands:
brew install cairo
brew install cairomm
brew install py2cairo
If "brew" ask you to run command or install other packages, do it !
(We assume here that "brew" is properly installed)
Best regards
I've faced the same issue (with a slight difference on the line number):
>>> from graph_tool.all import *
/usr/local/lib/python2.7/site-packages/graph_tool/draw/cairo_draw.py:1499: RuntimeWarning: Error importing Gtk module: No module named gi; GTK+ drawing will not work.
warnings.warn(msg, RuntimeWarning)
I know it's a relatively old question but wanted to share how I did it. You said you tried reinstalling GObject, but that is what made it work here.
I followed the installing instructions
brew install pygobject3 --with-python#2 gtk+3
which said gtk+3 and pygobject3 were already installed. Then I ran:
brew reinstall gtk+3
and
brew upgrade pygobject3
which made the import work.
I just have upgraded to os x 10.9 (clean install), but am finding issues with ghostscipt (or with X11-quartz). I need to view a dvi file (from latex) with this line command in Terminal
$ xdvi doc.dvi
The text appears fine, but the figures (.eps, .ps) do not show up. It left blank rectangles instaed. I get this error message
Warning: Unable to load any usable fontset
gs: Unknown device: x11
gs: Unrecoverable error: undefined in .uninstallpagedevice
gs: Operand stack:
gs: defaultdevice
xdvi-xaw: Warning: Read_from_gs returned 0 bytes
P.S. I installed XQuartz 2.7.5 (xorg-server 1.14.4), and GPL Ghostscript 9.07.
Any guidance please?
The first answer is correct, as re-installing MacTex should relink gs to gs-X11.
You can also just relink it yourself. For instance:
ls -l /usr/local/bin/gs
/usr/local/bin/gs -> /usr/local/bin/gs-noX11
sudo ln -sf /usr/local/bin/gs-X11 /usr/local/bin/gs
Now xdvi displays the images. Tested on Mavericks 10.9.4.
I reinstalled latex with MacTex again and now seems working fine.
Perhaps one needs to first install ghostscript then latex (?)
But note that I did some manipulations prior to this... In fact I reinstalled Ghostscript with mac ports. But even at that time it did not work, until I reinstalled Latex as highlighted above.
I am attempting to install the Cairo package in the development version of R on Mac OS X 10.7.4, but I'm running into an issue that I cannot resolve.
I have installed Cairo with homebrew (i.e., brew install cairo) and received the following message:
==> Caveats This formula is keg-only, so it was not symlinked into /usr/local.
Mac OS X already provides this program and installing another version
in parallel can cause all kinds of trouble.
The Cairo provided by Leopard is too old for newer software to link
against.
Generally there are no consequences of this for you. If you build your
own software and it requires this formula, you'll need to add its lib
& include paths to your build variables:
LDFLAGS -L/usr/local/Cellar/cairo/1.12.2/lib
CPPFLAGS -I/usr/local/Cellar/cairo/1.12.2/include
With the above message in mind, I attempted to install the Cairo package from R-Forge with the following R command:
install.packages("Cairo", repos="http://www.rforge.net/", configure.args = c("CAIRO_LIBS=/usr/local/Cellar/cairo/1.12.2/lib", "CAIRO_CFLAGS=/usr/local/Cellar/cairo/1.12.2/include/cairo"))
I receive the following error:
checking cairo.h usability... no
checking cairo.h presence... no
checking for cairo.h... no
configure: error: Cannot find cairo.h!
Please install cairo (http://www.cairographics.org/) and/or set
CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package ‘Cairo’
I repeated the same command without the repos argument (by default, I use the FHCRC mirror) with the same result.
At this point, the problem seems obvious: the file cairo.h is not present. But then I listed the files in the include/cairo directory. Here's the response:
ls /usr/local/Cellar/cairo/1.12.2/include/cairo
cairo-deprecated.h cairo-ft.h
cairo-ps.h
cairo-script-interpreter.h
cairo-svg.h
cairo-xcb.h
cairo-xlib.h
cairo-features.h
cairo-pdf.h
cairo-quartz.h
cairo-script.h
cairo-version.h
cairo-xlib-xrender.h
cairo.h
So, I'm pointing the installation of the Cairo package to the appropriate place, but the error persists. I have tried variations, such as CAIRO_CFLAGS=/usr/local/Cellar/cairo/1.12.2/include, with no luck.
Thoughts? Any help you can provide is greatly appreciated.
In case it's necessary, here is my sessionInfo:
R Under development (unstable) (2012-08-08 r60208) Platform: x86_64-apple-darwin11.4.0 (64-bit)
locale: [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] BiocInstaller_1.5.12
loaded via a namespace (and not attached): [1] tools_2.16.0
I had similar issue with cairo config error, and I already installed cairo with homebrew. Try below
brew install pkg-config
This solved mine problem.
A coworker and I just fixed the problem by ignoring all of what I typed above. Rather, we installed Cairo and all of its dependencies from source manually, thereby bypassing the usage of brew or variants like port. This worked like a charm, so I am not entirely sure what was wrong above.
After trying everything listed here, I found this blog post about installing the "full R package" using brew: https://luispuerto.net/blog/2018/05/11/installing-r-with-homebrew-with-all-the-capabilities/
What finally worked for me was building R explicitly with cairo (brew's default R tap uses --without-cairo and simply editing the tap did not solve the issue for me).
Works like a charm for me with R 4.0.2, cairo 1.16.0_3 under macOS Catalina 10.15.6.
I keep getting this error any time i call any page that has a call that uses RMagick, but i can't figure out what library i'm missing, or what i need to install to get rid of this error. Does anyone have debugging suggestions?
Processing SimpleCaptchaController#simple_captcha (for 127.0.0.1 at 2010-01-14 14:24:24) [GET]
Parameters: {"image_style"=>"", "time"=>"1263500664", "simple_captcha_key"=>"13eec13214d2ce84b725d14c5877fcbe13308cf5", "distortion"=>""}
Could not dump header data for exception: not opened for reading
ArgumentError (unknown format: JPG):
/usr/local/lib/ruby/gems/1.8/gems/fiveruns-dash-ruby-0.8.10/lib/fiveruns/dash/instrument.rb:125:in `perform_action_without_rescue'
...
After re-installing based on this cache of the bellow attempted solution
i am getting this error:
Magick::ImageMagickError (Wrong JPEG library version: library is 62, caller expects 70 `' # jpeg.c/EmitMessage/232):
I had to:
sudo port uninstall jpeg
install image magic using this script on git:
http://github.com/masterkain/ImageMagick-sl
after i was able to install rmagick:
sudo gem install rmagick
now, no more problems.
Their site is down at the moment, but when it comes back online you should run this install script by Solomon White.
http://onrails.org/articles/2009/09/04/rmagick-from-source-on-snow-leopard