only serial processing with windows, use map() instead of pool.map() for single thread in align and blur, remove deprecated blur functions, change pool and nprocs to private members, update plan, implement saving of aligned images, check if there's something to do

Author: pnuu

.travis.yml

@@ -8,6 +8,7 @@ python:
 before_install:
   - sudo apt-get update -qq
   - sudo apt-get install -qq python-numpy python-matplotlib python-pythonmagick
+  - sudo apt-get install --qq python3-matplotlib python3-numpy
 virtualenv:
   system_site_packages: true
 install:

bin/halostack_cli.py

@@ -29,6 +29,8 @@
                                get_two_points, read_config)
 import argparse
 import logging
+import platform
+import os
 
 # log pattern
 LOG_FMT = '%(asctime)s - %(name)s - %(levelname)s: %(message)s'
@@ -84,16 +86,12 @@ def halostack_cli(args):
 
     images = args['fname_in']
 
-    if len(images) == 0:
-        LOGGER.error("No images given.")
-        LOGGER.error("Exiting.")
-        return
-
     stacks = []
     for stack in args['stacks']:
         stacks.append(Stack(stack, len(images), nprocs=args['nprocs']))
 
-    base_img = Image(fname=images[0], nprocs=args['nprocs'])
+    base_img_fname = images[0]
+    base_img = Image(fname=base_img_fname, nprocs=args['nprocs'])
     LOGGER.debug("Using %s as base image.", base_img.fname)
     images.remove(images[0])
 
@@ -127,18 +125,24 @@ def halostack_cli(args):
         aligner.set_search_area(args['focus_area'])
         LOGGER.debug("Alignment initialized.")
 
+    if args['save_prefix'] is not None:
+        fname = args['save_prefix'] + '_' + \
+            os.path.splitext(base_img_fname)[0] + '.png'
+        base_img.save(fname)
+
     if len(args['enhance_images']) > 0:
         LOGGER.info("Preprocessing image.")
         base_img.enhance(args['enhance_images'])
+
     for stack in stacks:
         stack.add_image(base_img)
 
     # memory management
     del base_img
 
-    for img in images:
+    for img_fname in images:
         # Read image
-        img = Image(fname=img, nprocs=args['nprocs'])
+        img = Image(fname=img_fname, nprocs=args['nprocs'])
 
         if not args['no_alignment'] and len(images) > 1:
             # align image
@@ -148,9 +152,15 @@ def halostack_cli(args):
             LOGGER.warning("Skipping image.")
             continue
 
+        if args['save_prefix'] is not None:
+            fname = args['save_prefix'] + '_' + \
+                os.path.splitext(img_fname)[0] + '.png'
+            img.save(fname)
+
         if len(args['enhance_images']) > 0:
             LOGGER.info("Preprocessing image.")
             img.enhance(args['enhance_images'])
+
         for stack in stacks:
             stack.add_image(img)
 
@@ -178,7 +188,7 @@ def main():
                         dest="correlation_threshold",
                         default=None, metavar="NUM", type=float,
                         help="Minimum required correlation [0.7]")
-    parser.add_argument("-s", "--save-images", dest="save_postfix",
+    parser.add_argument("-s", "--save-images", dest="save_prefix",
                         default=None, metavar="STR",
                         help="Save aligned images as PNG with the given " \
                             "filename postfix")
@@ -229,6 +239,10 @@ def main():
         args['correlation_threshold'] = 0.7
     if not isinstance(args['no_alignment'], bool):
         args['no_alignment'] = False
+    if platform.system() == 'Windows':
+        LOGGER.warning("Your operting system is Windows, "
+                       "so limiting to one processor.")
+        args['nprocs'] = 1
 
     # Check which stacks will be made
     stacks = []
@@ -252,13 +266,19 @@ def main():
     args['stacks'] = stacks
     args['stack_fnames'] = stack_fnames
 
+    # Check if there's anything to do
+    if len(args['stacks']) == 0 and args['save_prefix'] is None or \
+            len(args['fname_in']) == 0:
+        LOGGER.error("Nothing to do.")
+        parser.print_help()
+        return
+
     LOGGER.info("Starting stacking")
 
     halostack_cli(args)
 
 
 if __name__ == "__main__":
-#    global LOGGER
     # Setup logging
     import logging.config
     logging.config.dictConfig(LOG_CONFIG)

doc/source/plan.rst

@@ -10,6 +10,9 @@ GUI
 
 - full graphical user interface
 
+  - help needed
+
+    - that is, need someone else to implement GUI
 
 Image input
 -----------
@@ -19,6 +22,13 @@ Image input
   - python-exif for linux, windows?
   - separate CSV file needed for TIFF and/or windows?
 
+- use Wand instead of PythonMagick
+
+  - provides also EXIF functionality
+
+- possibility to give directory containing all the photos
+- possibility to give image filenames/masks in config file
+
 
 Image alignment
 ------------------
@@ -47,9 +57,23 @@ Image enhancements
   - for example, several average stacks with different
     pre/postprocessing applied
 
-  - ``-a avg.png -a avg_pre_usm.png -e usm:25,2 -a avg_pre_post_usm.png -e usm:25,2 -E usm:25,2 -a avg_br.png -E gradient,br``
+  - ``-a avg.png -a avg_pre_usm.png -e usm:25,2 -a
+    avg_pre_post_usm.png -e usm:25,2 -E usm:25,2 -a avg_br.png -E
+    gradient,br``
 
 - bias subtraction
 - flat correction
 
   - for dust and vignetting removal
+
+- when applying to single image, skip Stack
+
+  - also remove requirement for command-line switch for a stack
+
+Python3
+-------
+
+- Get things ready for Python3
+
+  - replace PythonMagick with Wand
+  - check other parts

doc/source/usage.rst

@@ -139,6 +139,7 @@ ____________________
     - gradient removal (blurring)
 
   - default: ``1``
+  - unfortunately, in Windows you are limited to one thread
 
 - ``<list of filenames>``
 

halostack/align.py

@@ -56,13 +56,16 @@ def __init__(self, img, cor_th=70.0, mode='simple', nprocs=1):
 
         self.img = img
         self.correlation_threshold = cor_th
-        self.nprocs = nprocs
+        self._nprocs = nprocs
 
         self.ref_loc = None
         self.srch_area = None
         self.ref = None
 
-        self.pool = Pool(self.nprocs)
+        if self._nprocs > 1:
+            self._pool = Pool(self._nprocs)
+        else:
+            self._pool = None
 
         try:
             self.align_func = modes[mode]
@@ -156,7 +159,10 @@ def _parallel_search(self, img, xlims, ylims, ref_shp):
             xran = range(i-ref_shp[1], i+ref_shp[1]+1)
             data.append((img[:, xran], ylims, self.ref))
 
-        result = self.pool.map(_simple_search_worker, data)
+        if self._nprocs > 1:
+            result = self._pool.map(_simple_search_worker, data)
+        else:
+            result = map(_simple_search_worker, data)
 
         result = np.array(result)
         idx = np.argmin(result[:, 0])
@@ -195,7 +201,7 @@ def _simple_match(self, img):
                      ylims[0], ylims[1])
 
         LOGGER.debug("Searching for best match using %d thread(s).",
-                     self.nprocs)
+                     self._nprocs)
         best_res = self._parallel_search(img, xlims, ylims, ref_shp)
 
         # Calculate correlation coeff for the best fit