Merge pull request #1071 from griffithlab/vector_png

Fix blurry pVACvector visualization images
griffithlab · Mar 13, 2024 · d6e9acb · d6e9acb
2 parents dd495dd + 6f3db87
commit d6e9acb
Show file tree

Hide file tree

Showing 3 changed files with 13 additions and 7 deletions.
diff --git a/pvactools/lib/vector_visualization.py b/pvactools/lib/vector_visualization.py
@@ -1,6 +1,7 @@
 import turtle
 import os
 import sys
+import math
 from PIL import Image
 
 class VectorVisualization:
@@ -228,11 +229,16 @@ def draw_arc_junct(self, peptide, length):
     #print turtle screen to a postscript file, convert to pdf
     def output_screen(self):
         ps_file = os.path.join(self.output_directory, "vector.ps")
-        out_file = os.path.join(self.output_directory, "vector.jpg")
+        out_file = os.path.join(self.output_directory, "vector.png")
         ts = self.turtle.getscreen()
         ts.getcanvas().postscript(file=ps_file)
-        with Image.open(ps_file) as img:
-            img.save(out_file)
+        with Image.open(ps_file, formats=["EPS"]) as img:
+            original = [float(d) for d in img.size]
+            dpi = 300
+            scale = dpi / 72.0
+            img.load(scale = math.ceil(scale))
+            img.thumbnail([round(scale * d) for d in original], Image.Resampling.LANCZOS)
+            img.save(out_file, dpi=(300.0, 300.0))
         os.remove(ps_file)
 
     #select color from scheme

diff --git a/tests/test_pvacvector.py b/tests/test_pvacvector.py
@@ -191,7 +191,7 @@ def test_pvacvector_fa_input_runs_and_produces_expected_output(self):
             ))
 
             if 'DISPLAY' in os.environ.keys():
-                image_out = os.path.join(output_dir.name, 'vector.jpg')
+                image_out = os.path.join(output_dir.name, 'vector.png')
                 #vaccine visualization producing image
                 self.assertTrue(os.path.exists(image_out))
                 self.assertTrue(os.stat(image_out).st_size > 0)
@@ -226,7 +226,7 @@ def test_pvacvector_generate_fa_runs_and_produces_expected_output(self):
 
 
             if 'DISPLAY' in os.environ.keys():
-                image_out = os.path.join(output_dir.name, 'vector.jpg')
+                image_out = os.path.join(output_dir.name, 'vector.png')
                 #vaccine visualization producing image
                 self.assertTrue(os.path.exists(image_out))
                 self.assertTrue(os.stat(image_out).st_size > 0)

diff --git a/tests/test_vector_visualization.py b/tests/test_vector_visualization.py
@@ -28,7 +28,7 @@ def test_fasta_with_spacers(self):
                     output_dir,
                     self.spacers
                 ).draw())
-                self.assertTrue(os.path.exists(os.path.join(output_dir, 'vector.jpg')))
+                self.assertTrue(os.path.exists(os.path.join(output_dir, 'vector.png')))
 
     def test_fasta_with_long_peptide(self):
         if 'DISPLAY' in os.environ.keys():
@@ -41,4 +41,4 @@ def test_fasta_with_long_peptide(self):
                     output_dir,
                     self.spacers
                 ).draw())
-                self.assertTrue(os.path.exists(os.path.join(output_dir, 'vector.jpg')))
+                self.assertTrue(os.path.exists(os.path.join(output_dir, 'vector.png')))