Merge pull request #185 from jonwright/master

openmp threading defaults and fscan2d fixup

ImageD11/cImageD11.py

@@ -1,11 +1,13 @@
 # import cImageD11 compiled module and patch the docstrings
 
+import os
 import struct
 import warnings
 from ImageD11 import cImageD11_docstrings
 
 try:
     from ImageD11._cImageD11 import *
+    import ImageD11._cImageD11
 except ImportError:
     print("Failed to import compiled C code for cImageD11 module")
     print("Are you running from a source directory?")
@@ -37,7 +39,8 @@ def check_multiprocessing():
     if hasattr(multiprocessing,"parent_process"):
         parent = multiprocessing.parent_process()
         # only for python 3.8 and up
-        cimaged11_omp_set_num_threads( 1 ) 
+        if parent is not None:
+            cimaged11_omp_set_num_threads( 1 ) 
         # people wanting Nprocs * Mthreads need to reset after import
         # OMP_NUM_THREADS is not going to work for them
         # how are we going to remember this in the future??
@@ -52,7 +55,9 @@ def check_multiprocessing():
         # Tell them about it.
         warnings.warn(__doc__)
 
-
+def cores_available():
+    """ Return the number of CPU cores you can use """
+    return len( os.sched_getaffinity( os.getpid() ) )
 
 if cimaged11_omp_get_max_threads() == 0:
     # The code was compiled without openmp

ImageD11/sinograms/dataset.py

@@ -242,25 +242,28 @@ def guess_shape(self):
                 if title.split()[0] == 'fscan2d':
                     s0 = s['instrument/fscan_parameters/slow_npoints'][()]
                     s1 = s['instrument/fscan_parameters/fast_npoints'][()]
+                    file_nums = np.arange( s0 * s1 ).reshape( (s0,s1) ) 
+                    # slice notation means last frame+1 to be inclusive
+                    self.scans = [ "%s::[%d:%d]"%( self.scans[0], row[0], row[-1]+1 ) 
+                                    for row in file_nums ]
                 elif title.split()[0] == 'f2scan':
                     # good luck ? Assuming rotation was the inner loop here:
                     step = s['instrument/fscan_parameters/step_size'][()]
                     s1 = int( np.round( 360 / step ) )
                     s0 = npts // s1
+                    logging.warning("Dataset might need to be reshaped")
                 else:
                     s0 = 1
                     s1 = npts
-            # FIXME: we should reshape the omega/dty to match slow/fast points
-            #        also modify self.scans to be '4.1::[start:end]'
-        if len(self.scans) > 1:
+        elif len(self.scans) > 1:
             s0 = len(self.scans)
             s1 = npts // s0
         self.shape = s0, s1
         if np.prod( self.shape ) != npts:
             print("Warning: irregular scan - might be bugs in here")
             print(npts, len(self.scans))
-        self.omega = np.array( self.omega )
-        self.dty = np.array(self.dty )
+        self.omega = np.array( self.omega ).reshape( self.shape )
+        self.dty = np.array( self.dty ).reshape( self.shape )
         logging.info( 'sinogram shape = ( %d , %d ) imageshape = ( %d , %d)'%(
             self.shape[0], self.shape[1], self.imageshape[0], self.imageshape[1] ) )