Merge pull request #53 from decarlof/master

minor changes affecting APS 1-ID, 2-BM and 32-ID readers

dxchange/exchange.py

@@ -406,7 +406,7 @@ def read_aps_1id(fname, ind_tomo=None, proj=None, sino=None):
     # File definitions.
     fname = os.path.abspath(fname)
     _fname = fname + '000001.tif'
-    log_file = os.path.dirname(fname) + os.path.sep + 'TomoStillScan.dat'
+    log_file = fname + 'TomoStillScan.dat'
 
     # Read APS 1-ID log file data
     contents = open(log_file, 'r')
@@ -707,7 +707,8 @@ def read_aps_32id(fname, exchange_rank=0, proj=None, sino=None, dtype=None):
     theta = dxreader.read_hdf5(fname, theta_grp, slc=None)
 
     if (theta is None):
-        theta = np.linspace(0. , np.pi, tomo.shape[0])
+        theta_size = dxreader.read_dx_dims(fname, 'data')[0]
+        theta = np.linspace(0. , np.pi, theta_size)
     else:
         theta = theta * np.pi / 180.
     return tomo, flat, dark, theta

dxchange/reader.py

@@ -475,6 +475,33 @@ def read_edf(fname, slc=None):
     return arr
 
 
+def read_dx_dims(fname, dataset):
+    """
+    Read array size of a specific group of Data Exchange file.
+    Parameters
+    ----------
+    fname : str
+        String defining the path of file or file name.
+    dataset : str
+        Path to the dataset inside hdf5 file where data is located.
+    Returns
+    -------
+    ndarray
+        Data set size.
+    """
+
+    grp = '/'.join(['exchange', dataset])
+
+    with h5py.File(fname, "r") as f:
+        try:
+            data = f[grp]
+        except KeyError:
+            return None
+
+        shape = data.shape
+
+    return shape
+
 def read_hdf5(fname, dataset, slc=None, dtype=None, shared=False):
     """
     Read data from hdf5 file from a specific group.