Merge pull request #44 from skylarjhdownes/master

pep8 fixes and dependency documentation

doc/source/install.rst

@@ -2,7 +2,7 @@
 Install
 =======
 
-This section covers the basics of how to download and install 
+This section covers the basics of how to download and install
 `DXchange <https://github.com/data-exchange/dxchange>`_.
 
 .. contents:: Contents:
@@ -11,8 +11,8 @@ This section covers the basics of how to download and install
 
 Installing from source
 ======================
-  
-Clone the `DXchange <https://github.com/data-exchange/dxchange>`_  
+
+Clone the `DXchange <https://github.com/data-exchange/dxchange>`_
 from `GitHub <https://github.com>`_ repository::
 
     git clone https://github.com/data-exchange/dxchange.git dxchange
@@ -22,11 +22,13 @@ then::
     cd dxchange
     python setup.py install
 
+DXchange is dependent on other libraries, listed in the requirements.txt and
+meta.yaml files.
 
 Installing from Conda/Binstar
 =============================
 
-First you must have `Conda <http://continuum.io/downloads>`_ 
+First you must have `Conda <http://continuum.io/downloads>`_
 installed, then open a terminal or a command prompt window and run::
 
     conda install -c dgursoy dxchange
@@ -35,11 +37,11 @@ installed, then open a terminal or a command prompt window and run::
 Updating the installation
 =========================
 
-Data Management is an active project, so we suggest you update your installation 
+Data Management is an active project, so we suggest you update your installation
 frequently. To update the installation run in your terminal::
 
     conda update -c dgursoy dxchange
 
-For some more information about using Conda, please refer to the 
+For some more information about using Conda, please refer to the
 `docs <http://conda.pydata.org/docs>`__.
-    
+

dxchange/exchange.py

@@ -53,6 +53,11 @@
 from __future__ import (absolute_import, division, print_function,
                         unicode_literals)
 
+import numpy as np
+import os.path
+import re
+import logging
+import dxchange.reader as dxreader
 
 __authors__ = "Doga Gursoy, Luis Barroso-Luque, Francesco De Carlo"
 __copyright__ = "Copyright (c) 2015-2016, UChicago Argonne, LLC."
@@ -77,13 +82,6 @@
            'read_petraIII_p05',
            'read_sls_tomcat']
 
-
-import numpy as np
-import os.path
-import re
-import logging
-import dxchange.reader as dxreader
-
 logger = logging.getLogger(__name__)
 
 
@@ -309,11 +307,11 @@ def read_als_832h5(fname, ind_tomo=None, ind_flat=None, ind_dark=None,
         tomo = dxreader.read_hdf5_stack(
             dgroup, tomo_name, ind_tomo, slc=(proj, sino))
 
-        flat = dxreader.read_hdf5_stack(dgroup, flat_name, ind_flat, slc=(None, sino),
-                                        out_ind=group_flat)
+        flat = dxreader.read_hdf5_stack(
+            dgroup, flat_name, ind_flat, slc=(None, sino), out_ind=group_flat)
 
-        dark = dxreader.read_hdf5_stack(dgroup, dark_name, ind_dark, slc=(None, sino),
-                                        out_ind=group_dark)
+        dark = dxreader.read_hdf5_stack(
+            dgroup, dark_name, ind_dark, slc=(None, sino), out_ind=group_dark)
 
     return tomo, flat, dark, dxreader._map_loc(ind_tomo, group_flat)
 
@@ -740,9 +738,12 @@ def read_aus_microct(fname, ind_tomo, ind_flat, ind_dark, proj=None, sino=None):
     flat_name = os.path.join(fname, 'BG__BEFORE_00.tif')
     dark_name = os.path.join(fname, 'DF__BEFORE_00.tif')
 
-    tomo = dxreader.read_tiff_stack(tomo_name, ind=ind_tomo, digit=4, slc=(sino, proj))
-    flat = dxreader.read_tiff_stack(flat_name, ind=ind_flat, digit=2, slc=(sino, None))
-    dark = dxreader.read_tiff_stack(dark_name, ind=ind_dark, digit=2, slc=(sino, None))
+    tomo = dxreader.read_tiff_stack(
+        tomo_name, ind=ind_tomo, digit=4, slc=(sino, proj))
+    flat = dxreader.read_tiff_stack(
+        flat_name, ind=ind_flat, digit=2, slc=(sino, None))
+    dark = dxreader.read_tiff_stack(
+        dark_name, ind=ind_dark, digit=2, slc=(sino, None))
     return tomo, flat, dark
 
 

dxchange/reader.py

@@ -220,15 +220,6 @@ def read_xrm(fname, slice_range=None):
     else:
         slice_range = _make_slice_object_a_tuple(slice_range)
 
-    # if metadata["data_type"] == 10:
-    #     struct_fmt = "<{}f".format(
-    #         metadata["image_width"] * metadata["image_height"])
-    # elif metadata["data_type"] == 5:
-    #     struct_fmt = "<{}h".format(
-    #         metadata["image_width"] * metadata["image_height"])
-
-    # img = _read_ole_data(ole, "ImageData1/Image1", struct_fmt)
-
     stream = ole.openstream("ImageData1/Image1")
     data = stream.read()
 
@@ -248,7 +239,7 @@ def read_xrm(fname, slice_range=None):
     ole.close()
     return arr, metadata
 
-
+#  Should slc just take over what ind is doing here?
 def read_xrm_stack(fname, ind, slc=None):
     """
     Read data from stack of xrm files in a folder.
@@ -768,7 +759,7 @@ def _list_file_stack(fname, ind, digit=None):
         of the stacked files.
     """
 
-    if (digit is not None):
+    if digit is not None:
         warnings.warn(("The 'digit' argument is deprecated and no longer used."
                       "  It may be removed completely in a later version."),
                       FutureWarning)

test/test_dxchange/test_writer.py

@@ -54,22 +54,29 @@
 
 
 class remove_trailing_digits_test_case(unittest.TestCase):
-    def test_remove_trailing_digits_handles_not_having_digits(self):
-        text, digits = writer.remove_trailing_digits("someText")
-        assert_equal(text, "someText")
-
     def test_remove_trailing_digits_removes_zeroes(self):
-        text, digits = writer.remove_trailing_digits("someText0000")
+        text, number_of_digits = writer.remove_trailing_digits("someText0000")
         assert_equal(text, "someText")
 
     def test_remove_trailing_digits_removes_correct_number_of_zeroes(self):
-        text, digits = writer.remove_trailing_digits("someText0000")
-        assert_equal(digits, 4)
+        text, number_of_digits = writer.remove_trailing_digits("someText0000")
+        assert_equal(number_of_digits, 4)
 
     def test_remove_trailing_digits_removes_digits(self):
-        text, digits = writer.remove_trailing_digits("someText1234567890")
+        text, number_of_digits = writer.remove_trailing_digits(
+            "someText1234567890")
         assert_equal(text, "someText")
 
     def test_remove_trailing_digits_does_not_remove_digits_in_the_middle(self):
-        text, digits = writer.remove_trailing_digits("8s7o6m5e4T3e2x1t00.0000")
+        text, number_of_digits = writer.remove_trailing_digits(
+            "8s7o6m5e4T3e2x1t00.0000")
         assert_equal(text, "8s7o6m5e4T3e2x1t00.")
+
+    def test_remove_trailing_digits_handles_not_having_digits(self):
+        text, number_of_digits = writer.remove_trailing_digits("someText")
+        assert_equal(text, "someText")
+
+    def test_remove_trailing_digits_handles_empty_string(self):
+        text, number_of_digits = writer.remove_trailing_digits("")
+        assert_equal(text, "")
+        assert_equal(number_of_digits, 0)