Merge pull request #144 from kalinni/bug/magick

Updates ImageMagick to version 7 and makes its use platform independent

README.md

@@ -69,7 +69,7 @@ If you cannot use the containerized bundle or want to use PLIP sources, make sur
 - Python >= 3.6.9
 - [OpenBabel](#Installing-OpenBabel) >= 3.0.0 with [Python bindings](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html)
 - PyMOL >= 2.3.0 with Python bindings (optional, for visualization only)
-- ImageMagick >= 6.9 (optional)
+- ImageMagick >= 7.0 (optional)
 
 **Python:** If you are on a system where Python 3 is executed using `python3` instead of just `python`, replace the `python` and `pip` commands in the following steps with `python3` and `pip3` accordingly.
 
@@ -164,7 +164,7 @@ Using PLIP in your commercial or non-commercial project is generally possible wh
 If you are using PLIP in your work, please cite
 > Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA.
 > Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
- 
+
 or
 
 > Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.

plip/visualization/pymol.py

@@ -363,21 +363,29 @@ def png_workaround(filepath, width=1200, height=800):
         os.rename(originalfile, newfile)  # Remove frame number in filename
 
         #  Check if imagemagick is available and crop + resize the images
-        if subprocess.call("type convert", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
+        if subprocess.call("magick -version", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
             attempts, ecode = 0, 1
             # Check if file is truncated and wait if that's the case
             while ecode != 0 and attempts <= 10:
-                ecode = subprocess.call(['convert', newfile, '/dev/null'], stdout=open('/dev/null', 'w'),
+                ecode = subprocess.call(['magick', newfile, os.devnull], stdout=open(os.devnull, 'w'),
                                         stderr=subprocess.STDOUT)
                 sleep(0.1)
                 attempts += 1
-            trim = 'convert -trim ' + newfile + ' -bordercolor White -border 20x20 ' + newfile + ';'  # Trim the image
+            trim = f'magick {newfile} -trim -bordercolor White -border 20x20 {newfile}'  # Trim the image
             os.system(trim)
-            getwidth = 'w=`convert ' + newfile + ' -ping -format "%w" info:`;'  # Get the width of the new image
-            getheight = 'h=`convert ' + newfile + ' -ping -format "%h" info:`;'  # Get the hight of the new image
-            newres = 'if [ "$w" -gt "$h" ]; then newr="${w%.*}x$w"; else newr="${h%.*}x$h"; fi;'  # Set quadratic ratio
-            quadratic = 'convert ' + newfile + ' -gravity center -extent "$newr" ' + newfile  # Fill with whitespace
-            os.system(getwidth + getheight + newres + quadratic)
+            # Get the width of the new image
+            getwidth = f'magick {newfile} -ping -format "%w" info:'
+            w = int(subprocess.run(getwidth, capture_output=True, text=True).stdout)
+            # Get the hight of the new image
+            getheight = f'magick {newfile} -ping -format "%h" info:'
+            h = int(subprocess.run(getheight, capture_output=True, text=True).stdout)
+            # Set quadratic ratio
+            if w > h:
+                newr= f'{w}x{w}'
+            else:
+                newr= f'{h}x{h}'
+            quadratic = f'magick {newfile} -gravity center -extent {newr} {newfile}'  # Fill with whitespace
+            os.system(quadratic)
         else:
             sys.stderr.write('Imagemagick not available. Images will not be resized or cropped.')