support masking the intensity array + loglog plotting for the gui

6 files changed, 74 insertions, 20 deletions

diff --git a/BINoculars/.dispatcher.py.swo b/BINoculars/.dispatcher.py.swo
deleted file mode 100644
index 4d6f52e..0000000
--- a/BINoculars/.dispatcher.py.swo
+++ /dev/null
diff --git a/BINoculars/backends/id03.py b/BINoculars/backends/id03.py
index 434b81c..ad96e86 100644
--- a/BINoculars/backends/id03.py
+++ b/BINoculars/backends/id03.py
@@ -273,6 +273,7 @@ class ID03Input(backend.InputBase):
             self.config.xmask = slice(None)
         if self.config.ymask is None:
             self.config.ymask = slice(None)
+        self.config.maskmatrix = load_matrix(config.pop('maskmatrix', None)) #Optional, if supplied pixels where the mask is 0 will be removed
         if self.config.pr:
             self.config.pr = util.parse_tuple(self.config.pr, length=2, type=int)
         self.config.sdd = float(config.pop('sdd'))# sample to detector distance (mm)
@@ -458,6 +459,11 @@ class EH1(ID03Input):
         delta_range= app[0] * (numpy.arange(data.shape[0]) - centralpixel[0]) + delta
 
         # masking
+        if self.config.maskmatrix is not None:
+            if self.config.maskmatrix.shape != data.shape:
+                raise errors.BackendError('The mask matrix does not have the same shape as the images')
+            data = numpy.ma.array(data, mask = ~self.config.maskmatrix)
+
         gamma_range = gamma_range[self.config.ymask]
         delta_range = delta_range[self.config.xmask]
         intensity = self.apply_mask(data, self.config.xmask, self.config.ymask)
@@ -563,6 +569,12 @@ class EH2(ID03Input):
         delta_range = app[1] * (numpy.arange(data.shape[1]) - centralpixel[1]) + delta
 
         # masking
+
+        if self.config.maskmatrix is not None:
+            if self.config.maskmatrix.shape != data.shape:
+                raise errors.BackendError('The mask matrix does not have the same shape as the images')
+            data = numpy.ma.array(data, mask = ~self.config.maskmatrix)
+
         gamma_range = gamma_range[self.config.xmask]
         delta_range = delta_range[self.config.ymask]
         intensity = self.apply_mask(data, self.config.xmask, self.config.ymask)
@@ -574,7 +586,6 @@ class EH2(ID03Input):
         Phor = 1 - (numpy.sin(mu * numpy.pi / 180.) * numpy.sin(delta_grid * numpy.pi / 180.) * numpy.cos(gamma_grid* numpy.pi / 180.) + numpy.cos(mu* numpy.pi / 180.) * numpy.sin(gamma_grid* numpy.pi / 180.))**2
         intensity /= Phor
 
-
         return intensity, (wavelength, UB, gamma_range, delta_range, theta, mu, chi, phi)
 
     def get_point_params(self, scan, first, last):
diff --git a/BINoculars/plot.py b/BINoculars/plot.py
index 298ec52..713972c 100644
--- a/BINoculars/plot.py
+++ b/BINoculars/plot.py
@@ -101,7 +101,7 @@ def get_clipped_norm(data, clipping=0.0, log=True):
         return matplotlib.colors.Normalize(vmin, vmax)

 

 

-def plot(space, fig, ax, log=True, clipping=0.0, fit=None, norm=None, colorbar=True, labels=True, **plotopts):

+def plot(space, fig, ax, log=True, loglog = False, clipping=0.0, fit=None, norm=None, colorbar=True, labels=True, **plotopts):

     if space.dimension == 1:

         data = space.get_masked()

         xrange = numpy.ma.array(space.axes[0][:], mask=data.mask)

@@ -109,12 +109,17 @@ def plot(space, fig, ax, log=True, clipping=0.0, fit=None, norm=None, colorbar=T
             if log:

                 p1 = ax.semilogy(xrange, data, 'wo', **plotopts)

                 p2 = ax.semilogy(xrange, fit, 'r', linewidth=2, **plotopts)

+            elif loglog:

+                p1 = ax.loglog(xrange, data, 'wo', **plotopts)

+                p2 = ax.loglog(xrange, fit, 'r', linewidth=2, **plotopts)

             else:

                 p1 = ax.plot(xrange, data, 'wo', **plotopts)

                 p2 = ax.plot(xrange, fit, 'r', linewidth=2, **plotopts)

         else:

             if log:

                 p1 = ax.semilogy(xrange, data, **plotopts)

+            elif loglog:

+                p1 = ax.loglog(xrange, data, **plotopts)

             else:

                 p1 = ax.plot(xrange, data, **plotopts)

             p2 = []

diff --git a/BINoculars/space.py b/BINoculars/space.py
index 44fafb5..b74c4a1 100644
--- a/BINoculars/space.py
+++ b/BINoculars/space.py
@@ -585,7 +585,13 @@ class Space(object):
         if len(coordinates) != len(self.axes):
             raise ValueError('dimension mismatch between coordinates and axes')
 
-        valid = numpy.isfinite(intensity)
+        if isinstance(intensity, numpy.ma.core.MaskedArray):
+            mask = intensity.mask
+            intensity = intensity.data
+        else:
+            mask = numpy.ones_like(intensity)
+
+        valid = numpy.bitwise_and(numpy.isfinite(intensity), ~mask)
         intensity = intensity[valid]
         if not intensity.size:
             return
@@ -610,6 +616,7 @@ class Space(object):
         labels          n-tuple of axis labels
         coordinates   n-tuple of data coordinate arrays
         intensity     data intensity array"""
+
         axes = tuple(Axis(coord.min(), coord.max(), res, label) for res, label, coord in zip(resolutions, labels, coordinates))
         newspace = cls(axes)
         newspace.process_image(coordinates, intensity)
@@ -763,10 +770,18 @@ def axis_offset(space, label, offset):
     return space.transform_coordinates((ax.res for ax in space.axes), (ax.label for ax in space.axes), transformation)
 
 def bkgsubtract(space, bkg):
-    bkg.photons = bkg.photons * space.contributions / bkg.contributions
-    bkg.photons[bkg.contributions == 0] = 0
-    bkg.contributions = space.contributions
-    return space - bkg
+    if space.dimension == bkg.dimension:
+        bkg.photons = bkg.photons * space.contributions / bkg.contributions
+        bkg.photons[bkg.contributions == 0] = 0
+        bkg.contributions = space.contributions
+        return space - bkg
+    else:
+        photons = numpy.broadcast_arrays(space.photons, bkg.photons)[1]
+        contributions = numpy.broadcast_arrays(space.contributions, bkg.contributions)[1]
+        bkg = Space(space.axes)
+        bkg.photons = photons
+        bkg.contributions = contributions
+        return bkgsubtract(space, bkg)
 
 def make_compatible(spaces):
     if not numpy.alen(numpy.unique(len(space.axes) for space in spaces)) == 1:    
diff --git a/gui.py b/gui.py
index 50868d5..237bbf8 100644
--- a/gui.py
+++ b/gui.py
@@ -387,9 +387,22 @@ class ProjectWidget(QtGui.QWidget):
         self.canvas = FigureCanvasQTAgg(self.figure)
         self.toolbar = HiddenToolbar(self.show_coords,self.update_sliders, self.canvas)
 
-        self.log = QtGui.QCheckBox('log', self)
+        self.lin = QtGui.QRadioButton('lin', self)
+        self.lin.setChecked(False)
+        QtCore.QObject.connect(self.lin, QtCore.SIGNAL("toggled(bool)"), self.plot)
+
+        self.log = QtGui.QRadioButton('log', self)
         self.log.setChecked(True)
-        QtCore.QObject.connect(self.log, QtCore.SIGNAL("stateChanged(int)"), self.plot)
+        QtCore.QObject.connect(self.log, QtCore.SIGNAL("toggled(bool)"), self.plot)
+
+        self.loglog = QtGui.QRadioButton('loglog', self)
+        self.loglog.setChecked(False)
+        QtCore.QObject.connect(self.loglog, QtCore.SIGNAL("toggled(bool)"), self.plot)
+
+        self.loggroup = QtGui.QButtonGroup(self)
+        self.loggroup.addButton(self.lin)
+        self.loggroup.addButton(self.log)
+        self.loggroup.addButton(self.loglog)
 
         self.swap_axes = QtGui.QCheckBox('swap axes', self)
         self.swap_axes.setChecked(False)
@@ -433,8 +446,6 @@ class ProjectWidget(QtGui.QWidget):
         self.control_widget = QtGui.QWidget(self)
         hbox = QtGui.QHBoxLayout() 
         left = QtGui.QVBoxLayout()
-        radiobox =  QtGui.QHBoxLayout() 
-
         left.addWidget(self.button_save)
 
         radiobox =  QtGui.QHBoxLayout() 
@@ -444,13 +455,15 @@ class ProjectWidget(QtGui.QWidget):
             self.group.addButton(rb)
             radiobox.addWidget(rb)
 
+        radiobox.addWidget(self.lin)
+        radiobox.addWidget(self.log)
+        radiobox.addWidget(self.loglog)
+
         datarangebox = QtGui.QHBoxLayout() 
-        datarangebox.addWidget(self.log)
         datarangebox.addWidget(self.samerange)
         datarangebox.addWidget(self.legend)
         datarangebox.addWidget(self.swap_axes)
 
-
         left.addLayout(radiobox)
         left.addLayout(datarangebox)
         left.addWidget(self.datarange)
@@ -520,14 +533,16 @@ class ProjectWidget(QtGui.QWidget):
             self.datarange.setDisabled(True)
             self.samerange.setDisabled(True)
             self.swap_axes.setDisabled(True)
+            self.loglog.setEnabled(True)
         elif len(self.limitwidget.sliders) - len(self.projection) == 2:
+            self.loglog.setDisabled(True)
             self.datarange.setEnabled(True)
             self.samerange.setEnabled(True)
             self.swap_axes.setEnabled(True)
         self.plot()
 
     def get_norm(self, mi, ma):
-        log = self.log.checkState()
+        log = self.log.isChecked()
 
         rangemin = self.datarange.low() * 1.0 / self.datarange.maximum()
         rangemax = self.datarange.high() * 1.0 / self.datarange.maximum()
@@ -546,7 +561,7 @@ class ProjectWidget(QtGui.QWidget):
             return matplotlib.colors.Normalize(vmin, vmax)
 
     def get_normlist(self):
-        log = self.log.checkState()
+        log = self.log.isChecked()
         same = self.samerange.checkState()
 
         if same:
@@ -562,7 +577,8 @@ class ProjectWidget(QtGui.QWidget):
         self.parent.statusbar.clearMessage()
 
         self.figure_images = []
-        log = self.log.checkState()
+        log = self.log.isChecked()
+        loglog = self.loglog.isChecked()
 
         plotcount = len(self.table.selection)
         plotcolumns = int(numpy.ceil(numpy.sqrt(plotcount)))
@@ -587,7 +603,7 @@ class ProjectWidget(QtGui.QWidget):
         self.datamax = []
         for space in spaces:
             data = space.get_masked().compressed()
-            if log:
+            if log or loglog:
                 data = data[data > 0]
             self.datamin.append(data.min())
             self.datamax.append(data.max())
@@ -616,7 +632,7 @@ class ProjectWidget(QtGui.QWidget):
                 space = space.reorder(list(ax.label for ax in space.axes)[::-1])
 
             self.ax.space = space
-            im = BINoculars.plot.plot(space,self.figure, self.ax, log = log,label = basename, norm = norm[i])         
+            im = BINoculars.plot.plot(space, self.figure, self.ax, log = log, loglog = loglog, label = basename, norm = norm[i])         
 
             self.figure_images.append(im)
         
diff --git a/test/id03.py b/test/id03.py
index 6b365e8..e7fed8c 100644
--- a/test/id03.py
+++ b/test/id03.py
@@ -1,6 +1,8 @@
 from BINoculars.backends import id03
 import BINoculars.util
+import BINoculars.space
 import os
+import numpy
 
 import unittest
 
@@ -13,6 +15,8 @@ class TestCase(unittest.TestCase):
         cfg_unparsed['pixelsize'] = '0.055, 0.055'
         cfg_unparsed['imagefolder'] = specfile.replace('sixc_tutorial.spec', 'images')
         cfg_unparsed['centralpixel'] = '50 ,50'
+        numpy.save('mask.npy', numpy.identity(516))
+        cfg_unparsed['maskmatrix'] = 'mask.npy'
         self.id03input = id03.EH2(cfg_unparsed)
         self.projection = id03.pixels({'resolution' : '1'})
 
@@ -20,10 +24,13 @@ class TestCase(unittest.TestCase):
         jobs = list(self.id03input.generate_jobs(['820']))
         destination_opts = self.id03input.get_destination_options(['820'])
         imagedata = self.id03input.process_job(jobs[0])
-        self.projection.project(*imagedata.next()[1])
+        intensity, coords = imagedata.next()
+        projected = self.projection.project(*coords)
+        space = BINoculars.space.Space.from_image((1,1), ('x','y'), projected, intensity)
+        print space
 
     def tearDown(self):
-        pass
+        os.remove('mask.npy')
   
 if __name__ == '__main__':
     unittest.main()