diff pp_dexela.py @ 0:4d2a2268a17a draft

"planemo upload"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pp_dexela.py	Thu Sep 23 21:00:48 2021 +0000
@@ -0,0 +1,153 @@
+from __future__ import print_function
+
+import time
+import os
+import numpy as np
+
+from hexrd import imageseries
+from hexrd.imageseries.process import ProcessedImageSeries
+
+
+
+
+class ProcessedDexelaIMS(ProcessedImageSeries):
+
+    ADDROW = 'add-row'
+    ADDCOL = 'add-column'
+
+    def __init__(self, imser, oplist, **kwargs):
+        super(ProcessedDexelaIMS, self).__init__(imser, oplist, **kwargs)
+        self.addop(self.ADDROW, self._addrow)
+        self.addop(self.ADDCOL, self._addcol)
+
+    def _addrow(self, img, k):
+        """insert row into position k"""
+        shp = img.shape
+        pimg = np.insert(img, k, 0, axis=0)
+        if k==0:
+            pimg[0] = pimg[1]
+        elif k==shp[0]:
+            pimg[k] = pimg[k-1]
+        else: # in middle
+            pimg[k] = (pimg[k-1] + pimg[k+1])/2
+
+        return pimg
+
+    def _addcol(self, img, k):
+        """insert row into position k"""
+        shp = img.shape
+        pimg = np.insert(img, k, 0, axis=1)
+        if k==0:
+            pimg[:,0] = pimg[:,1]
+        elif k==shp[0]:
+            pimg[:,k] = pimg[:,k-1]
+        else: # in middle
+            pimg[:,k] = (pimg[:,k-1] + pimg[:,k+1])/2
+
+        return pimg
+
+
+DexelaIMS=ProcessedDexelaIMS
+
+class PP_Dexela(object):
+    """PP_Dexela"""
+    PROCFMT = 'frame-cache'
+    RAWFMT = 'hdf5'
+    RAWPATH = '/imageseries'
+    DARKPCTILE = 50
+
+    def __init__(self,
+                 fname, omw, panel_opts, panel_id,
+                 frame_start=0, raw_format='hdf5',dark=None):
+        """Constructor for PP_Dexela"""
+        self._panel_id = panel_id
+        self.fname = fname
+        self.omwedges = omw
+        self.panel_opts = panel_opts
+        self.frame_start = frame_start
+        self.use_frame_list = (self.frame_start > 0)
+        if raw_format.lower() == 'hdf5':
+            self.raw = imageseries.open(
+                self.fname, self.RAWFMT, path=self.RAWPATH
+                )
+        else:
+            self.raw = imageseries.open(self.fname, raw_format.lower())
+        self._dark = dark
+
+        #print(
+        #    'On Init:\n\t%s, %d frames, %d omw, %d total'
+        #    % (self.fname, self.nframes, self.omwedges.nframes, len(self.raw))
+        #)
+
+    @property
+    def panel_id(self):
+        return self._panel_id
+
+    @property
+    def oplist(self):
+        return [('dark', self.dark)]+self.panel_opts
+
+    @property
+    def framelist(self):
+        return range(self.frame_start, self.nframes + self.frame_start)
+
+    #
+    # ============================== API
+    #
+    @property
+    def nframes(self):
+        return self.omwedges.nframes
+
+    @property
+    def omegas(self):
+        return self.omwedges.omegas
+
+    def processed(self):
+        kw = {}
+        if self.use_frame_list:
+            kw = dict(frame_list=self.framelist)
+        return DexelaIMS(self.raw, self.oplist, **kw)
+
+    @property
+    def dark(self, nframes=100):
+        """build and return dark image"""
+        if self._dark is None:
+            usenframes = min(nframes, self.nframes)
+            print(
+                "building dark images using %s frames (may take a while)..."
+                % usenframes
+            )
+            start = time.time()
+#            self._dark = imageseries.stats.percentile(
+#                    self.raw, self.DARKPCTILE, nframes=usenframes
+#            )
+            self._dark = imageseries.stats.median(
+                    self.raw, nframes=usenframes
+            )#changed to median by DCP 11/18/17
+            elapsed = (time.time() - start)
+            print(
+                "done building background (dark) image: " +
+                "elapsed time is %f seconds" % elapsed
+            )
+
+        return self._dark
+
+    def save_processed(self, name, threshold, output_dir=None):
+        if output_dir is None:
+            output_dir = os.getcwd()
+        else:
+            os.mkdir(output_dir)
+
+        # add omegas
+        pims = self.processed()
+        metad = pims.metadata
+        metad['omega'] = self.omegas
+        metad['panel_id'] = self.panel_id
+        cache = '%s-cachefile.npz' % name
+        imageseries.write(pims, "dummy", self.PROCFMT,
+                          style="npz",
+                          threshold=threshold,
+                          cache_file=cache)
+    pass  # end class
+
+