Release 0.2.0

emtools/__init__.py

@@ -24,5 +24,5 @@
 # *
 # **************************************************************************
 
-__version__ = '0.1.3'
+__version__ = '0.2.0-rc260805'
 

emtools/datatypes.py

@@ -0,0 +1,21 @@
+# **************************************************************************
+# *
+# * Authors:     J.M. de la Rosa Trevin (delarosatrevin@gmail.com)
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# **************************************************************************
+
+
+"""Shared data-type labels for EM file and workflow object metadata."""
+
+VOLUME = 'Volume'
+STACK_2D = '2D stack'

emtools/image/__init__.py

@@ -1,8 +1,6 @@
 # **************************************************************************
 # *
-# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
-# *
-# * [1] SciLifeLab, Stockholm University
+# * Authors:     J.M. de la Rosa Trevin (delarosatrevin@gmail.com)
 # *
 # * This program is free software; you can redistribute it and/or modify
 # * it under the terms of the GNU General Public License as published by
@@ -14,18 +12,11 @@
 # * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # * GNU General Public License for more details.
 # *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'delarosatrevin@scilifelab.se'
-# *
 # **************************************************************************
 
 
-from .thumbnail import Thumbnail
+from .thumbnail import Thumbnail, Image
+from emtools.datatypes import STACK_2D, VOLUME
 
 
-__all__ = [Thumbnail]
+__all__ = ["Thumbnail", "Image", "STACK_2D", "VOLUME"]

emtools/image/__main__.py

@@ -0,0 +1,97 @@
+# **************************************************************************
+# *
+# * Authors:     J.M. de la Rosa Trevin (delarosatrevin@gmail.com)
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 3 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# **************************************************************************
+
+import argparse
+import mrcfile
+import numpy as np
+
+from .thumbnail import Image, Thumbnail
+
+
+
+def show2D(inputFile, **kwargs):
+    import matplotlib.pyplot as plt
+    size = kwargs.get('size', 512)
+    print("size: ", size)
+    thumb = Thumbnail(max_size=(size, size), contrast_factor=0.15, std_threshold=1)
+    array = Image.get_array(inputFile)
+    plt.imshow(thumb.from_array(array), cmap='gray')
+    plt.axis('off')  # Optional: Turn off axis labels and ticks
+    plt.show()
+
+
+def fourier_crop(inputFile, scale):
+    array = Image.get_array(inputFile)
+    return Image.fourier_crop(inputFile, scale)
+
+
+def save_array(array, outputFile):
+    if outputFile.endswith('.mrc'):
+        with mrcfile.new(outputFile, overwrite=True) as mrc:
+            mrc.set_data(array)
+    elif outputFile.endswith('.png'):
+        thumb = Thumbnail(max_size=None, contrast_factor=0.15)#, std_threshold=1)
+        pil_img = thumb.from_array(array)
+        pil_img.save(outputFile)
+    else:
+        raise ValueError(f"Unsupported file type: {outputFile}")
+    return outputFile
+
+
+def compare_images(inputFile1, inputFile2):
+    array1 = Image.get_array(inputFile1)
+    array2 = Image.get_array(inputFile2)
+    return np.array_equal(array1, array2)
+
+
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument('path', metavar="IMAGE_PATH",
+                   help="Image path")
+    p.add_argument('--show', '-s', action='store_true',
+                   help="Show the image")
+    p.add_argument('--max-size', '-m', type=int, default=512,
+                   help="Size of the image")
+    p.add_argument('--bin', '-b', type=float, default=None,
+                  help="Bin factor for the image, using Fourier cropping. Bin 1 means no cropping, bin 2 means half the original size, etc.")
+    p.add_argument('--output', '-o', type=str, default=None,
+                  help="Output file name")
+    p.add_argument('--compare', '-c', 
+                  help="Compare the image with another image.")
+    args = p.parse_args()
+
+    if args.show:
+        show2D(args.path, size=args.max_size)
+    elif args.bin:
+        if args.bin > 1:
+            scale = 1 / args.bin
+            array = fourier_crop(args.path, scale)
+            if args.output:
+                save_array(array, args.output)
+        else:
+            print("Bin factor must be greater than 1")
+    elif args.compare:
+        if compare_images(args.path, args.compare):
+            print("Images are the same")
+        else:
+            print("Images are different")
+    else:
+        print(Image.get_dimensions(args.path))
+
+
+if __name__ == '__main__':
+    main()