Merge pull request #528 from vallsv/backport-to-0.13

Backport from 0.14-dev to 0.13

.travis.yml

@@ -26,7 +26,6 @@ addons:
       - libqtcore4
 #For OpenCL:
       - libboost1.48-dev
-      - libboost-python-dev
       - libboost-python1.48
       - opencl-headers
       - python-pyopencl

doc/source/changelog.rst

@@ -5,6 +5,14 @@
 ChangeLog of Versions
 =====================
 
+0.13.1: 30/01/2017
+------------------
+
+* Backport critical bug fix from 0.14-dev
+    - Convert matplotlib mouse input into pixel coordinates (fix issue with numpy 0.12)
+    - Fix eiger-mask script if h5py is not installed
+    - Use "/usr/bin/env python" for scripts
+
 0.13.0: 01/12/2016
 ------------------
 * Global improvement of tests, packaging, code quality, documentation and project tools

pyFAI/massif.py

@@ -26,7 +26,7 @@
 __contact__ = "[email protected]"
 __license__ = "GPLv3+"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "24/11/2016"
+__date__ = "12/12/2016"
 __status__ = "production"
 
 import sys
@@ -113,7 +113,8 @@ def find_peaks(self, x, nmax=200, annotate=None, massif_contour=None, stdout=sys
         """
         All in one function that finds a maximum from the given seed (x)
         then calculates the region extension and extract position of the neighboring peaks.
-        :param x: seed for the calculation, input coordinates
+        :param x: coordinates of the peak, seed for the calculation
+        :type x: tuple of integer
         :param nmax: maximum number of peak per region
         :param annotate: call back method taking number of points + coordinate as input.
         :param massif_contour: callback to show the contour of a massif with the given index.

pyFAI/peak_picker.py

@@ -27,7 +27,7 @@
 __contact__ = "[email protected]"
 __license__ = "GPLv3+"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "27/10/2016"
+__date__ = "12/12/2016"
 __status__ = "production"
 
 import os
@@ -413,23 +413,28 @@ def common_creation(points, gpt=None):
             return gpt
 
         def new_grp(event):
-            " * Right-click (click+n):         try an auto find for a ring"
-            points = self.massif.find_peaks([event.ydata, event.xdata],
+            " * new_grp Right-click (click+n):         try an auto find for a ring"
+            # ydata is a float, and matplotlib display pixels centered.
+            # we use floor (int cast) instead of round to avoid use of
+            # banker's rounding
+            ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
+            points = self.massif.find_peaks([ypix, xpix],
                                             self.defaultNbPoints,
                                             None, self.massif_contour)
             if points:
                 gpt = common_creation(points)
-                annontate(points[0], [event.ydata, event.xdata], gpt=gpt)
+                annontate(points[0], [ypix, xpix], gpt=gpt)
                 logger.info("Created group #%2s with %i points", gpt.label, len(gpt))
             else:
                 logger.warning("No peak found !!!")
 
         def single_point(event):
             " * Right-click + Ctrl (click+b):  create new group with one single point"
-            newpeak = self.massif.nearest_peak([event.ydata, event.xdata])
+            ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
+            newpeak = self.massif.nearest_peak([ypix, xpix])
             if newpeak:
                 gpt = common_creation([newpeak])
-                annontate(newpeak, [event.ydata, event.xdata], gpt=gpt)
+                annontate(newpeak, [ypix, xpix], gpt=gpt)
                 logger.info("Create group #%2s with single point x=%5.1f, y=%5.1f", gpt.label, newpeak[1], newpeak[0])
             else:
                 logger.warning("No peak found !!!")
@@ -445,8 +450,10 @@ def append_more_points(event):
                     self.ax.lines.remove(gpt.plot[0])
 
             update_fig(self.fig)
+            # matplotlib coord to pixel coord, avoinding use of banker's round
+            ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
             # need to annotate only if a new group:
-            listpeak = self.massif.find_peaks([event.ydata, event.xdata],
+            listpeak = self.massif.find_peaks([ypix, xpix],
                                               self.defaultNbPoints, None,
                                               self.massif_contour)
             if listpeak:
@@ -466,7 +473,9 @@ def append_1_point(event):
                 if gpt.plot[0] in self.ax.lines:
                     self.ax.lines.remove(gpt.plot[0])
             update_fig(self.fig)
-            newpeak = self.massif.nearest_peak([event.ydata, event.xdata])
+            # matplotlib coord to pixel coord, avoinding use of banker's round
+            ypix, xpix = int(event.ydata + 0.5), int(event.xdata + 0.5)
+            newpeak = self.massif.nearest_peak([ypix, xpix])
             if newpeak:
                 gpt.points.append(newpeak)
                 logger.info("x=%5.1f, y=%5.1f added to group #%2s", newpeak[1], newpeak[0], gpt.label)
@@ -511,8 +520,8 @@ def erase_1_point(event):
                     self.ax.lines.remove(gpt.plot[0])
             if len(gpt) > 1:
                 # delete single closest point from current group
-                x0 = event.xdata
-                y0 = event.ydata
+                # matplotlib coord to pixel coord, avoinding use of banker's round
+                y0, x0 = int(event.ydata + 0.5), int(event.xdata + 0.5)
                 distsq = [((p[1] - x0) ** 2 + (p[0] - y0) ** 2) for p in gpt.points]
                 # index and distance of smallest distance:
                 indexMin = min(enumerate(distsq), key=operator.itemgetter(1))

scripts/eiger-mask

@@ -35,20 +35,28 @@ __author__ = "Jerome Kieffer"
 __contact__ = "[email protected]"
 __license__ = "GPLv3+"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "28/11/2016"
+__date__ = "05/12/2016"
 __satus__ = "development"
 
 
 import os
 import sys
-import h5py
+import logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger("eiger-mask")
 import numpy
 import fabio
+
 try:
     from argparse import ArgumentParser
 except ImportError:
     from pyFAI.third_party.argparse import ArgumentParser
 
+try:
+    import h5py
+except ImportError:
+    h5py = None
+
 
 def extract_mask(infile):
     """
@@ -65,11 +73,18 @@ def extract_mask(infile):
 
 if __name__ == "__main__":
     description = "A tool to extract the mask from an Eiger detector file."
-    parser = ArgumentParser(description=description)
+    epilog = None
+    if h5py is None:
+        epilog = "Python h5py module is missing. It have to be installed to use this application"
+    parser = ArgumentParser(description=description, epilog=epilog)
     parser.add_argument('input_file', help='Input file. Must be an HDF5 file.')
     parser.add_argument('output_file', nargs="?", help='Output file. It can be an msk, tif, or an edf file.')
     options = parser.parse_args()
 
+    if h5py is None:
+        logger.error("Python h5py module is expected to use this script")
+        sys.exit(1)
+
     infile = os.path.abspath(options.input_file)
     if options.output_file is not None:
         outfile = options.output_file

setup.cfg

@@ -6,3 +6,5 @@
 #For Windows with Cuda 64 bits:
 #include-dirs: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v3.2\include
 #library-dirs: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v3.2\lib\x64
+[build]
+executable = /usr/bin/env python

version.py

@@ -53,7 +53,7 @@
 __authors__ = ["Jérôme Kieffer"]
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "02/12/2016"
+__date__ = "30/01/2017"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 __all__ = ["date", "version_info", "strictversion", "hexversion", "debianversion", "calc_hexversion"]
@@ -67,7 +67,7 @@
 
 MAJOR = 0
 MINOR = 13
-MICRO = 0
+MICRO = 1
 RELEV = "final"  # <16
 SERIAL = 0  # <16