updates for wxpython 4 compatability

Author: joelvbernier

conda.recipe/meta.yaml

@@ -4,7 +4,7 @@ package:
 
 source:
   #git_url: https://github.com/joelvbernier/hexrd.git
-  #git_tag: v0.3.x
+  #git_tag: v0.6.x
   git_url: ../
 
 build:
@@ -22,15 +22,15 @@ requirements:
   build:
     - numba
     - numpy
-    - python ==2
+    - python
     - setuptools
   run:
     - h5py
     - matplotlib
     - numba
     - numpy
     - progressbar
-    - python ==2
+    - python
     - python.app # [osx]
     - pyyaml
     - scikit-image
@@ -41,17 +41,17 @@ requirements:
 test:
   imports:
     - hexrd
-   #commands:
-   #  - hexrd -V
-   #  - hexrd -h
-   #  - hexrd help
-   #  - hexrd find-orientations -h
-   #  - hexrd help find-orientations
-   #  - hexrd fit-grains -h
-   #  - hexrd help fit-grains
-   #  - hexrd gui -h
-   #  - hexrd help gui
-   #  - hexrd test
+   # commands:
+   #   - hexrd -V
+   #   - hexrd -h
+   #   - hexrd help
+   #   - hexrd find-orientations -h
+   #   - hexrd help find-orientations
+   #   - hexrd fit-grains -h
+   #   - hexrd help fit-grains
+   #   - hexrd gui -h
+   #   - hexrd help gui
+   #   - hexrd test
 
 about:
   license: LGPL

docs/build.rst

@@ -22,8 +22,6 @@ Building
 First, the dependencies for building an environment to run hexrd::
 
     - cython
-    - dask
-    - distributed
     - fabio <pip>
     - h5py
     - matplotlib
@@ -36,21 +34,26 @@ First, the dependencies for building an environment to run hexrd::
     - scikit-image
     - scikit-learn
     - scipy
-    - wxpython ==3
+    - wxpython
 
 If you will be running scripts of you own, I also strongly suggest adding spyder::
 
     - spyder
 
 For example, to buid an environment to run hexrd v0.6.x, do the following::
 
-    conda create --name hexrd_0.6 cython dask distributed h5py matplotlib numba numpy=1.15 progressbar=2.3 python=2.7 pyyaml setuptools scikit-image scikit-learn scipy spyder wxpython=3
+    conda create --name hexrd_0.6 cython h5py matplotlib numba numpy python=2.7 pyyaml setuptools scikit-image scikit-learn scipy spyder
+    conda install -c anaconda --name hexrd_0.6 wxpython
+    conda install -c anaconda --name hexrd_0.6 progressbar
+    conda activate hexrd_0.6
+    
 
-Then install in develop mode using disutils::
+Then install using setuptools::
   
-    python setup.py develop
+    python setup.py install
     
-The procedure for building/installing with conda-build is as follows
+Note, you will have to install fabio in the same environment using ``setup.py`` as well.
+The procedure for building/installing with conda-build is as follows (*this is curently broken*)
 
 First, update conda and conda-build::
 
@@ -106,4 +109,4 @@ directory) and run::
 
     hexrd --verison
 
-It should currently read ``hexrd 0.6.0``
+It should currently read ``hexrd 0.6.5``

hexrd/findorientations.py

@@ -26,9 +26,7 @@
 
 from hexrd.fitgrains import get_instrument_parameters
 
-logger = logging.getLogger(__name__)
-
-save_as_ascii = False  # FIX LATER...
+from skimage.feature import blob_dog, blob_log
 
 # just require scikit-learn?
 have_sklearn = False
@@ -43,9 +41,20 @@
     pass
 
 
+method = "blob_dog"  # !!! have to get this from the config
+save_as_ascii = False  # FIX LATER...
+
+logger = logging.getLogger(__name__)
+
+
+# =============================================================================
+# FUNCTIONS
+# =============================================================================
+
+
 def generate_orientation_fibers(
         eta_ome, chi, threshold, seed_hkl_ids, fiber_ndiv,
-        filt_stdev=0.8, ncpus=1):
+        method='blob_dog', filt_stdev=0.8, ncpus=1):
     """
     From ome-eta maps and hklid spec, generate list of
     quaternions from fibers
@@ -82,21 +91,42 @@ def generate_orientation_fibers(
     numSpots = []
     coms = []
     for i in seed_hkl_ids:
-        # First apply filter
-        this_map_f = -ndimage.filters.gaussian_laplace(
-            eta_ome.dataStore[i], filt_stdev)
-
-        labels_t, numSpots_t = ndimage.label(
-            this_map_f > threshold,
-            structureNDI_label
-            )
-        coms_t = np.atleast_2d(
-            ndimage.center_of_mass(
-                this_map_f,
-                labels=labels_t,
-                index=np.arange(1, np.amax(labels_t)+1)
+        if method == 'label':
+            # First apply filter
+            this_map_f = -ndimage.filters.gaussian_laplace(
+                eta_ome.dataStore[i], filt_stdev)
+            
+            labels_t, numSpots_t = ndimage.label(
+                this_map_f > threshold,
+                structureNDI_label
                 )
-            )
+            coms_t = np.atleast_2d(
+                ndimage.center_of_mass(
+                    this_map_f,
+                    labels=labels_t,
+                    index=np.arange(1, np.amax(labels_t) + 1)
+                    )
+                )
+        elif method in ['blob_log', 'blob_dog']:
+            # must scale map
+            this_map = eta_ome.dataStore[i]
+            this_map[np.isnan(this_map)] = 0.
+            this_map -= np.min(this_map)
+            scl_map = 2*this_map/np.max(this_map) - 1.
+
+            # FIXME: need to expose the parameters to config options.
+            if method == 'blob_log':
+                blobs = np.atleast_2d(
+                    blob_log(scl_map, min_sigma=0.5, max_sigma=5,
+                             num_sigma=10, threshold=0.01, overlap=0.1)
+                )
+            else:
+                blobs = np.atleast_2d(
+                    blob_dog(scl_map, min_sigma=0.5, max_sigma=5,
+                             sigma_ratio=1.6, threshold=0.01, overlap=0.1)
+                    )
+            numSpots_t = len(blobs)
+            coms_t = blobs[:, :2]
         numSpots.append(numSpots_t)
         coms.append(coms_t)
         pass

hexrd/instrument.py

@@ -55,7 +55,7 @@
                                       mapAngle, \
                                       oscillAnglesOfHKLs, \
                                       rowNorm, \
-                                      validateAngleRanges
+                                      unitRowVector
 from hexrd.xrd import xrdutil
 from hexrd.xrd.crystallography import PlaneData
 from hexrd import constants as ct
@@ -554,10 +554,11 @@ def extract_polar_maps(self, plane_data, imgser_dict,
                         # remap
                         retas = mapAngle(retas, new_period)
                         tmp_bins = mapAngle(eta_edges[reta_idx], new_period)
-                        reta_idx = np.argsort(tmp_bins)
+                        tmp_idx = np.argsort(tmp_bins)
+                        reta_idx = reta_idx[np.argsort(tmp_bins)]
                         eta_bins = np.hstack(
-                            [tmp_bins[reta_idx],
-                             tmp_bins[reta_idx][-1] + delta_eta]
+                            [tmp_bins[tmp_idx],
+                             tmp_bins[tmp_idx][-1] + delta_eta]
                         )
                         pass
                     pass
@@ -600,7 +601,7 @@ def extract_line_positions(self, plane_data, imgser_dict,
             tth_ranges = np.degrees(plane_data.getMergedRanges()[1])
             tth_tols = np.vstack([i[1] - i[0] for i in tth_ranges])
         else:
-            tth_tols=np.ones(len(plane_data))*tth_tol
+            tth_tols = np.ones(len(plane_data))*tth_tol
 
         # =====================================================================
         # LOOP OVER DETECTORS
@@ -624,7 +625,8 @@ def extract_line_positions(self, plane_data, imgser_dict,
 
             # make rings
             pow_angs, pow_xys = panel.make_powder_rings(
-                plane_data, merge_hkls=True, delta_tth=tth_tol, delta_eta=eta_tol)
+                plane_data, merge_hkls=True,
+                delta_tth=tth_tol, delta_eta=eta_tol)
 
             # =================================================================
             # LOOP OVER RING SETS
@@ -681,7 +683,7 @@ def extract_line_positions(self, plane_data, imgser_dict,
                         ims_data = []
                     for j_p in np.arange(len(images)):
                         # catch interpolation type
-                        image=images[j_p]
+                        image = images[j_p]
                         if do_interpolation:
                             tmp = panel.interpolate_bilinear(
                                     xy_eval,
@@ -1552,13 +1554,13 @@ def clip_to_panel(self, xy, buffer_edges=True):
                     )
                     on_panel = np.logical_and(on_panel_x, on_panel_y)
             elif not buffer_edges:
-                    on_panel_x = np.logical_and(
-                        xy[:, 0] >= -xlim, xy[:, 0] <= xlim
-                    )
-                    on_panel_y = np.logical_and(
-                        xy[:, 1] >= -ylim, xy[:, 1] <= ylim
-                    )
-                    on_panel = np.logical_and(on_panel_x, on_panel_y)
+                on_panel_x = np.logical_and(
+                    xy[:, 0] >= -xlim, xy[:, 0] <= xlim
+                )
+                on_panel_y = np.logical_and(
+                    xy[:, 1] >= -ylim, xy[:, 1] <= ylim
+                )
+                on_panel = np.logical_and(on_panel_x, on_panel_y)
         return xy[on_panel, :], on_panel
 
     def cart_to_angles(self, xy_data):
@@ -1743,7 +1745,7 @@ def make_powder_rings(
         eta_centers = eta_edges[:-1] + del_eta
 
         # !!! get chi and ome from rmat_s
-        chi = np.arctan2(rmat_s[2, 1], rmat_s[1, 1])
+        # chi = np.arctan2(rmat_s[2, 1], rmat_s[1, 1])
         ome = np.arctan2(rmat_s[0, 2], rmat_s[0, 0])
 
         # make list of angle tuples

hexrd/wx/fitparampanel.py

@@ -97,12 +97,12 @@ def __makeObjects(self):
     def __makeTitleBar(self, t):
         """Add titlebar"""
         self.titlebar = wx.StaticText(self, -1, t,
-                                         style=wx.ALIGN_CENTER|wx.SIMPLE_BORDER)
+                                      style=wx.ALIGN_CENTER|wx.SIMPLE_BORDER)
         self.titlebar.SetBackgroundColour(WP.TITLEBAR_BG_COLOR)
         myToolTip = r"""
-PANEL FOR managing data for fit parameters
-"""
-        self.titlebar.SetToolTipString(myToolTip)
+        PANEL FOR managing data for fit parameters
+        """
+        self.titlebar.SetToolTip(myToolTip)
 
         return
 

hexrd/wx/floatcontrol.py

@@ -98,7 +98,7 @@ def __init__(self, parent, id, **kwargs):
 The spinner increment is shown in the gray
 box to the right of the spinner.
 """
-        self.SetToolTipString(myToolTip)
+        self.SetToolTip(myToolTip)
 
         self.SetAutoLayout(True)
         self.SetSizerAndFit(self.sizer)

hexrd/wx/guiutil.py

@@ -111,7 +111,7 @@ def makeTitleBar(p, t, **kwargs):
     #  Keyword args
     #
     tt = 'tooltip'
-    if tt in kwargs:  titlebar.SetToolTipString(kwargs[tt])
+    if tt in kwargs:  titlebar.SetToolTip(kwargs[tt])
 
     cl = 'color'
     if cl in kwargs:

hexrd/wx/indexpanel.py

@@ -204,7 +204,7 @@ def __makeObjects(self):
 
         self.friedel_cbox = wx.CheckBox(self, wx.NewId(), 'Friedel Only')
         self.friedel_cbox.SetValue(iopts.friedelOnly)
-        self.claims_cbox = wx.CheckBox(self, wx.NewId(), 'Preserve Claiims')
+        self.claims_cbox = wx.CheckBox(self, wx.NewId(), 'Preserve Claims')
         self.claims_cbox.SetValue(iopts.preserveClaims)
         self.refine_cbox  = wx.CheckBox(self, wx.NewId(), 'Do Refinement')
         self.refine_cbox.SetValue(iopts.doRefinement)

hexrd/wx/listeditor.py

@@ -101,7 +101,7 @@ def __makeTitleBar(self, t):
         myToolTip = r"""
 PANEL FOR ...
 """
-        self.titlebar.SetToolTipString(myToolTip)
+        self.titlebar.SetToolTip(myToolTip)
 
         return
 

hexrd/wx/materialspanel.py

@@ -189,7 +189,7 @@ def __makeTitleBar(self, t):
         myToolTip = r"""
 PANEL FOR ...
 """
-        self.titlebar.SetToolTipString(myToolTip)
+        self.titlebar.SetToolTip(myToolTip)
 
         return