So when I try to use imread on a TIFF-file, it raises this error.
The TIFF-file in question is a TIFF I created and modified in another script. I initially created it like this: temp = np.full([max_y, max_x], np.nan). Then I looped the cells and changed the cell values. Afterwards I used cv2.imwrite to write it to a file.
However the original script where I create and modify the TIFF-file also opens it after writing the file so no clue why it opens then, and not in this new script. The only change I've made since then is copying the file.
I can also open the file in QGIS so no clue what the problem is.
EDIT: this is the picture https://drive.google.com/file/d/1CjAGegeA9RUmTtgd_8xgrRPqOLx8NdMa/view?usp=sharing
The relevant part of the code you can find here: https://codeshare.io/5oYNDo.
The error occurs in line 32.
EDIT 2: With the help of Mark I've got it transformed to a 32-bit image: https://drive.google.com/file/d/1xDyqeEzMrB-84ms9BB7YztbT-_kfJpeG/view?usp=sharing. However plt.imread still didn't work. So now I am using img_arr = np.asarray(Image.open(img)). However this results in a strange bug: the array is full of NaN's but when I hover over a picture I do get the cell value. (https://imgur.com/a/jbppYuO) Because of the array full of NaN's vmin and vmax are not working properly, that's why the whole picture is yellow. If I remove the vmin and vmax it's visualized as it should. But the array full of NaN's will result in problems further in the script so this has to be solved first.
Your image is a 64-bit floating point TIFF. You can see that with:
tiffinfo v3l1_24-34.tiff
Or with ImageMagick:
magick identify -verbose v3l1_24-34.tiff
PIL doesn't like such things, so you either need to either create it as 32-bit:
temp = np.full(..., dtype=np.float32)
or, if you need 64-bit, maybe read it with tifffile:
import tifffile
...
im = tiffffile.imread('v3l1_24-34.tiff')
If you have some pre-existing BigTIFF files you want to make into 32-bit classic TIFF files, you can try the following commands:
# Use an ImageMagick version with Q16 or higher and HDRI when you run "identify -version"
magick input.tif -define quantum:format=floating-point -depth 32 output.tif
# Or use "libvips" in the Terminal
vips im_vips2tiff input.tif output.tif
To check if a file is a BigTIFF or not, use exiftool and look for BTF like this:
exiftool bigtiff.tif
ExifTool Version Number : 11.11
File Name : bigtiff.tif
Directory : .
File Size : 1024 kB
File Modification Date/Time : 2020:03:13 13:56:05+00:00
File Access Date/Time : 2020:03:13 13:56:19+00:00
File Inode Change Date/Time : 2020:03:13 13:56:11+00:00
File Permissions : rw-r--r--
File Type : BTF <--- HERE
...
...
Or use xxd like this and look for 3rd byte being 0x2b:
xxd bigtiff.tif | more
00000000: 4949 2b00 0800 0000 1000 1000 0000 0000 II+.............
...
...
whereas a ClassicTIFF shows up as 0x2a:
xxd classic.tiff | more
00000000: 4949 2a00 0800 1000 0000 803f 0000 803f II*........?...?
Related
I am using pstoedit as a part of a shell script to convert svg to dxf.
When I use pstoedit -psarg '-dNOSAFER' -dt -f 'dxf: -mm' "${epsfile}" "${dxffile}" in script, the result is like the picture below.
But when i use pstoedit -psarg '-dNOSAFER' -dt -f 'dxf_14: -mm' "${epsfile}" "${dxffile}" the result is like the picture below.
See the difference? dxf gives complete lines, but dxf_14 gives small lines not connected. I read pstohedit -help and it mentions to use dxf_14 because it's newer, but I can't if it's going to produce results like this.
I also see a bunch of options specific to dxf_14, but I'm not sure what to use. Can anyone guide me on what switches to use for dxf_14 to get desired result, like the first picture above?
PS. I'm using Inkscape to create svg and then the script converts svg to eps using inkscape cli and the pstoedit is used to convert eps to dxf, if it helps.
PS2. pstoedit version is pstoedit: version 3.74 / DLL interface 108 (built: Oct 31 2019 - release build - g++ 9.2.0 - 64-bit)
I developing pdf conversion app with node.js and Ghostscript. I execute command line gs with exec(). My command definition looks like:
let gs_cmd = `
gs -sDEVICE=pdfwrite \
-dPDFX=true \
-dPDFACompatibilityPolicy=1 \
-sColorConversionStrategy=/CMYK \
-sProcessColorModel=DeviceCMYK \
-sDefaultCMYKProfile=${icc_profile_file} \
-dNoOutputFonts \
-dBATCH \
-dQUIET \
-r${DPI} \
-g${w}x${h} \
-dPDFFitPage \
-NumRenderingThreads=4 \
-o ${target_file}-conv.pdf \
PDFX_def.ps \
#trimbox.in "Trimed" \
${target_file}.pdf
`;
I have problem with line:
#trimbox.in "Trimed" \
which tells to Ghostscript to include file and pass the parameters to in. I can't find a proper way to include parameters that can be used in included file. I want to pass "Trimed" string as $0 argument which will be available in trimbox.in file. I also tried with -t=Trimmed or -t="Trimmed" without effects.
From Ghostscript docs (section 10.1):
#filename
Causes Ghostscript to read filename and treat its contents the same as the command line. (This was intended primarily for getting around DOS's 128-character limit on the length of a command line.) Switches or file names in the file may be separated by any amount of white space (space, tab, line break); there is no limit on the size of the file.
-- filename arg1 ...
-+ filename arg1 ...
Takes the next argument as a file name as usual, but takes all remaining arguments (even if they have the syntactic form of switches) and defines the name ARGUMENTS in userdict (not systemdict) as an array of those strings, before running the file. When Ghostscript finishes executing the file, it exits back to the shell.
How to achieve this?
Running my command causes error:
Error: /undefined in Trimed
Firstly you should review the Ghostscript licence to ensure your use is compliant with the licence (AGPL v3). Note that this includes software as a service applications.
"Trimed" isn't a Ghostscript switch and it isn't the name of an input file, so yes, you get an error. You can't 'pass parameters' to #file, because Ghostscript treats that, literally, as a file containing a bunch of switches. There is no command substitution or anything like that. SO you can't have $0 in the file specified by #file.
So when you say :
#PDFX_def_trimbox.ps "Trimed" \
which tells to Ghostscript to include file and pass the parameters to
in
I'm afraid you are incorrect. There is no way to 'pass parameters' to the file when using the #file syntax.
You haven't said what's in the file 'PDFX_def_trimbox.ps', and I'm suspicious (because of the .ps) that this is a PostScript program. You can't use a PostScript program with the #file syntax, because a PostScript program is not a series of Ghostscript switches.
So where you have :
-sDEVICE=pdfwrite \
-dPDFX=true\
etc, you could put all of those switches into the file specified by #file. But you can't put any PostScript in there.
There are a few other problems. You have specified NumRenderingThreads=4, which will do nothing, because the pdfwrite device doesn't (in general) do any rendering, it preserves the input as far as possible as vector data. So pdfwrite ignores this parameter altogether.
For similar reasons, the -r parameter is less than useful. In the case of pdfwrite that simply affects how accurate the conversion is. You shouldn't set that without good reason.
You've set -sColorConversionStrategy=/CMYK when it should be =-sColorConversionStrategy=CMYK or -dColorConversionStrategy=/CMYK. -s takes strings, -d takes numbers or names.
-g sets teh widht and height of the page in pixels, which isn't a great plan, that depends on the resolution. You should -dDEVICEWIDTHPOINTS and -dDEVICEHEIGHTPOINTS instead, and not set the resolution.
-EDIT-
-response to comment below-
If you want PDF file to contain a 300 dpi image, then you need to create a page which is the correct size so that, when drawn on it, the bitmap data form the image is 300 dpi.
So for example, if you have an image which is 600 pixels by 900 pixels, then in order to get that to be 300 dpi you must make the media size 2 inches by 3 inches, which is 144 by 216 points. Changing the resolution of the pdfwrite device won't affect that at all. Setting -g and -r will alter the media size, but not the resolution of the image, though if you also set -dPDFFitPage then yes it will rescale the image to fit the media, which will alter its resolution.....
I have no idea if your original image was 300 dpi, if it was, and the SVG to PDF conversion maintained that, then you don't need to mess about with media sizes and resolution at all, the pdfwrite device will maintain whatever was there.
As regards the #file syntax, you cannot do this:
-c "[ {ThisPage} << /TrimBox [$0 $1 $2 $3] >> /PUT pdfmark"
in the file supplied via the # comamnd because, as I said, there is no variable replacement in the processing which Ghostscript does on the contents of that file. This is not a bash script.
I use a program which create me postscript file before using ps2pdf to make it a readable pdf, i've made a program which add some string to overwrite the company new logo. (The first program can't import image file itself).
I add the string before the before-last line of the file (" showpage").
While running my program to add the logo there is no error.
With the option -dNOSAFER everything is fine, but by default it's set to -dSAFER, and an invalidfileaccess error pop, the files are 6 jpg images alone in their directory.
I don't want to make it run with the -dNOSAFER option on. As it will fully open the file system.
In the documentation I've seen that there is a "permitted path" setting, but i can't find nowhere to set this up. Is it just a command line option to set in the command launching the program ? Or is there a config file for GhostScript / ps2pdf where i can put the path to this directory as permitted path.
in this documentation :
http://www.ghostscript.com/doc/current/Use.htm
I only find
-dTTYPAUSE
Causes Ghostscript to read a character from /dev/tty, rather than
standard input, at the end of each page. This may be useful if input
is coming from a pipe. Note that -dTTYPAUSE overrides -dNOPAUSE. Also
note that -dTTYPAUSE requires opening the terminal device directly,
and may cause problems in combination with -dSAFER. Permission errors
can be avoided by adding the device to the permitted reading list
before invoking safer mode
gs -dTTYPAUSE -dDELAYSAFER -c '<< /PermitFileReading [ (/dev/tty)] >> setuserparams .locksafe' -dSAFER
The quote is just for the context but is this a way to put the permitted path ?
As gs automatically launch with the full system as readOnly there will be no difference ? There is no other find result for PermitFile in this page.
Try adding the required path to the search path with -I (Include) See Use.htm, section 8 How Ghostscript finds files. This should only be a problem if you are using 'run' or similar to read files from another location.
The section on TTYPAUSE is not relevant.
I am attempting to convert a directory full of .bmp files into a .mp4 file (or similar format).
The bitmap files have the following name scheme:
output_N_1024.bmp
Where N is an integer in the range 0 to 1023. (No zero padding / fixed width.)
The command I am using is:
avconv -r 25 -i output_{0..1023}_1024.bmp outputfile.mp4
This appears to run okay, and takes about a minute to convert all 1024, 1024 by 1024 resolution - (confusing?) bitmap images into a new file, outputfile.mp4.
However, when I attempt to open this file with VLC, a black window briefly flashes up and then closes. VLC then goes back to its mode where it waits for you to tell it which file to open next. No error or warning messages appear from VLC, which seems kind of strange since it seems to be refusing to play.
What can I do to fix this? Perhaps my converting command is incorrect?
The problem most likely is that you haven't actually passed the command to encode these files to avconv. This has happened because your shell has expanded the filenames already.
The command i have just managed to get to work on my machine is:
avconv -r 2 -i "%d.bmp" -s 600x400 -an out.ogv
Also for whatever reason it didn't want to work without explicitely giving it the size, but i don't think this is your problem.
In here quotes tell your shell not to touch this string. %d means digits from 1 to whatever the last file is (if you would want them to be 0-padded this would look like %000d to have maximum of three naughts in front).
VLC has then opened and ran my file just fine.
I've written a program to process a bunch of png files that are generated by a seperate process. The capture mostly works, however there are times when the process dies and is restarting which leaves a corrupted image. I have no way to detect when the process dies or which file it dies one (there are ~3000 png files).
Is there a good way to check for a corrupted png file?
I know this is a question from 2010, but I think this is a better solution: pngcheck.
Since you're on a Linux system you probably already have Python installed.
An easy way would be to try loading and verifying the files with PIL (Python Imaging Library) (you'd need to install that first).
from PIL import Image
v_image = Image.open(file)
v_image.verify()
(taken verbatim from my own answer in this thread)
A different possible solution would be to slightly change how your processor processes the files: Have it always create a file named temp.png (for example), and then rename it to the "correct" name once it's done. That way, you know if there is a file named temp.png around, then the process got interrupted, whereas if there is no such file, then everything is good.
(A variant naming scheme would be to do what Firefox's downloader does -- append .partial to the real filename to get the temporary name.)
Kind of a hack, but works
If you are running on linux or something like you might have the "convert" command
$ convert --help
Version: ImageMagick 5.5.6 04/01/03 Q16 http://www.imagemagick.org
Copyright: Copyright (C) 2003 ImageMagick Studio LLC
Usage: convert [options ...] file [ [options ...] file ...] [options ...] file
If you make an invalid png, and then try to convert, you'll get an error:
$ date> foo.png
$ convert foo.png foo.gif
convert: NotAPNGImageFile (foo.png).
Find all non-PNG files:
find . -type f -print0 | xargs -0 file --mime | grep -vF image/png
Find all corrupted PNG files:
find . -type f -print0 | xargs -0 -P0 sh -c 'magick identify +ping "$#" > /dev/null' sh
file command only checks magic number. Having the PNG magic number doesn't mean it is a well formed PNG file.
magick identify is a tool from ImageMagick. By default, it only checks headers of the file for better performance. Here we use +ping to disable the feature and make identify read the whole file.