Release 0.2.0

emtools/__init__.py

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

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 +12,10 @@
 # * 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
 
 
-__all__ = [Thumbnail]
+__all__ = ["Thumbnail", "Image"]

emtools/image/__main__.py

@@ -0,0 +1,32 @@
+# **************************************************************************
+# *
+# * 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
+from .thumbnail import Image
+
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument('path', metavar="IMAGE_PATH",
+                   help="Image path")
+
+    args = p.parse_args()
+
+    print(Image.get_dimensions(args.path))
+
+
+if __name__ == '__main__':
+    main()

emtools/image/thumbnail.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
@@ -14,22 +12,19 @@
 # * 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 doctest import OutputChecker
 import io
 import numpy as np
 import base64
 import mrcfile
+import tifffile
 
-from PIL import Image, ImageOps, ImageFilter
+import PIL
+from PIL import Image
+
+from emtools.utils import Path, Pretty
 
 
 class Thumbnail:
@@ -49,7 +44,6 @@ def __init__(self, **kwargs):
         self.min_max = kwargs.get('min_max', None)
         self.std_threshold = kwargs.get('std_threshold', 0)
 
-
     def __format(self, pil_img):
         format = self.output_format
 
@@ -79,18 +73,18 @@ def from_pil(self, pil_img):
         self.scale = scale
 
         if self.contrast_factor is not None:
-            pil_img = ImageOps.autocontrast(pil_img, cutoff=self.contrast_factor)
+            pil_img = PIL.ImageOps.autocontrast(pil_img, cutoff=self.contrast_factor)
 
         if self.gaussian_radius is not None:
-            pil_img = pil_img.filter(ImageFilter.GaussianBlur(radius=self.gaussian_radius))
+            pil_img = pil_img.filter(PIL.ImageFilter.GaussianBlur(radius=self.gaussian_radius))
 
         return self.__format(pil_img)
 
     def from_path(self, path):
         """ Read the image path as a PIL image and encode it as base64.
         """
         try:
-            img = Image.open(path)
+            img = PIL.Image.open(path)
             encoded = self.from_pil(img)
             img.close()
         except:
@@ -121,7 +115,7 @@ def from_array(self, imageArray):
 
         im255 = ((array - iMin) / (iMax - iMin) * 255).astype(np.uint8)
 
-        pil_img = Image.fromarray(im255)
+        pil_img = PIL.Image.fromarray(im255)
 
         return self.from_pil(pil_img)
 
@@ -143,8 +137,8 @@ def from_mrc(self, mrc_path):
 
     @staticmethod
     def Micrograph(**kwargs):
-        """ Shortcut method with presets for Micrograph thumbail.
-        All settings can be overwriten with kwargs.
+        """ Shortcut method with presets for Micrograph thumbnail.
+        All settings can be overwritten with kwargs.
         """
         defaults = {
             'output_format': 'base64',
@@ -157,8 +151,8 @@ def Micrograph(**kwargs):
 
     @staticmethod
     def Psd(**kwargs):
-        """ Shortcut method with presets for PSD thumbails.
-        All settings can be overwriten with kwargs.
+        """ Shortcut method with presets for PSD thumbnails.
+        All settings can be overwritten with kwargs.
         """
         defaults = {
             'output_format': 'base64',
@@ -168,3 +162,80 @@ def Psd(**kwargs):
         defaults.update(kwargs)
         return Thumbnail(**defaults)
 
+    @staticmethod
+    def Preview(imagePath, **kwargs):
+        imageLower = imagePath.lower()
+        thumb = Thumbnail.Micrograph(max_size=(256, 256))
+
+        if not (Path.isImage(imagePath) or Path.isEmImage(imagePath)):
+            raise Exception("Can not generate preview for: %s" % imagePath)
+
+        if Path.isImage(imagePath):
+            return thumb.from_path(imagePath)
+
+        if imageLower.endswith('.mrc'):
+            dims = Image.get_dimensions(imagePath)
+            mrc = mrcfile.open(imagePath, permissive=True)
+            thumb = Thumbnail.Micrograph()
+            if len(dims) == 2:
+                array = mrc.data 
+            elif len(dims) == 3:
+                x, y, z = dims
+                if mrc.is_volume() or (x == y and y == z):
+                    thumb = Thumbnail(max_size=(256, 256), output_format='base64')
+                    iMax = mrc.data.max()  # min(imean + 10 * isd, imageArray.max())
+                    iMin = mrc.data.min()  # max(imean - 10 * isd, imageArray.min())
+                    im255 = ((mrc.data - iMin) / (iMax - iMin) * 255).astype(np.uint8)
+
+                    # 1. Setup
+                    ximg = PIL.Image.fromarray(im255[:, :, x // 2])
+                    yimg = PIL.Image.fromarray(im255[:, y // 2, :])
+                    zimg = PIL.Image.fromarray(im255[z // 2, :, :])
+
+                    xw, xh = ximg.size
+                    yw, yh = yimg.size
+                    zw, zh = zimg.size
+
+                    pad = 2  # The thickness of the dark gray lines/borders
+
+                    # 2. Calculate canvas size for a full grid with outer borders
+                    # Total Width = (2 * image width) + (3 * padding for left, middle, right)
+                    canvas_w = (xw + yw) + (3 * pad)
+                    canvas_h = (xh + zh) + (3 * pad)
+
+                    # Create canvas with a white background (matching your image)
+                    bg_color = (256, 256, 256) 
+                    montage = PIL.Image.new('RGB', (canvas_w, canvas_h), bg_color)
+
+                    # Top-Left: x slice
+                    montage.paste(ximg, (pad, pad))                    
+                    # Bottom-Left: z slice
+                    montage.paste(zimg, (pad, xh + 2 * pad))
+                    # Bottom-Right: y slice
+                    montage.paste(yimg, (xw + 2 * pad, xh + 2 * pad))
+
+                    return thumb.from_pil(montage)
+                    Pretty.dprint("Loading MRC volume: %s" % str(array.shape))
+                else:
+                    array = mrc.data[z//2, :, :] # FIXME
+                    Pretty.dprint("Loading MRC 2D: %s" % str(array.shape))
+                return thumb.from_array(array)
+            else:
+                raise Exception("Invalid dimensions: %s" % dims)
+
+
+class Image:
+    @staticmethod
+    def get_dimensions(imagePath):
+        imageLower = imagePath.lower()
+        if imageLower.endswith('.mrc') or imageLower.endswith('.mrcs'):
+            with mrcfile.open(imagePath) as mrc:
+                return mrc.data.shape[::-1]  # in reverse order
+        elif (imageLower.endswith('.tif') or
+              imageLower.endswith('.tiff') or
+              imageLower.endswith('.eer') or
+              imageLower.endswith('.gain')):
+            with tifffile.TiffFile(imagePath) as tif:
+                n = len(tif.pages)
+                y, x = tif.pages[0].shape
+                return (x, y, n) if n > 1 else (x, y)

emtools/jobs/__init__.py

@@ -14,7 +14,11 @@
 # *
 # **************************************************************************
 
-from .pipeline import Pipeline, ProcessingPipeline
-from .batch_manager import BatchManager
+from .pipeline import Pipeline
+from .batch_manager import (Args, Batch, Vars,
+                            BatchManager, MdocBatchManager, TsStarBatchManager)
+from .workflow import Workflow
 
-__all__ = ["Pipeline", "BatchManager", "ProcessingPipeline"]
+__all__ = ["Pipeline", "Workflow",
+           "Args", "Vars",
+           "Batch", "BatchManager", "MdocBatchManager", "TsStarBatchManager"]