From 4d5fd3886c14dccf87d8d0f9dc5ba10d89804290 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@desy.de>
Date: Tue, 6 Jun 2017 20:45:25 +0200
Subject: [PATCH] Fixed some bugs, added some checks and documentation

---
 cfel_cxi.py                            |  43 +++++++++++++++++--------
 doc/build/doctrees/cfelpyutils.doctree | Bin 135019 -> 137275 bytes
 doc/build/doctrees/environment.pickle  | Bin 12789 -> 12789 bytes
 doc/build/html/cfelpyutils.html        |   8 ++---
 doc/build/html/searchindex.js          |   2 +-
 5 files changed, 34 insertions(+), 19 deletions(-)

diff --git a/cfel_cxi.py b/cfel_cxi.py
index 7263d45..8076f96 100644
--- a/cfel_cxi.py
+++ b/cfel_cxi.py
@@ -25,20 +25,29 @@ from __future__ import division
 from __future__ import print_function
 from __future__ import unicode_literals
 
-from builtins import str
-
 from collections import namedtuple
 import h5py
+import numpy
 
 _CXISimpleEntry = namedtuple('SimpleEntry', ['path', 'data', 'overwrite'])
 
+def _assign_data_type(data):
+
+    if isinstance(data, numpy.ndarray):
+        data_type = data.dtype
+    elif isinstance(data, bytes):
+        data_type = numpy.dtype('S256')
+    else:
+        data_type = type(data)
+
+    return data_type
 
 class _Stack:
     def __init__(self, path, data, axes, compression, chunk_size):
 
-        self._data_type = type(data)
+        self._data_type = _assign_data_type(data)
 
-        if isinstance(data, (str, int, float)):
+        if isinstance(data, (bytes, int, float)):
             self._data_shape = (1,)
         else:
             self._data_shape = data.shape
@@ -63,9 +72,12 @@ class _Stack:
     def write_initial_slice(self, file_handle, max_num_slices):
 
         file_handle.create_dataset(self.path, shape=(max_num_slices,) + self._data_shape,
+                                   dtype = self._data_type,
                                    maxshape=(max_num_slices,) + self._data_shape,
                                    compression=self._compression, chunks=self._chunk_size)
-        file_handle[self.path][0] = self._data_to_write
+
+        dataset = file_handle[self.path]
+        dataset[0] = self._data_to_write
 
         if self._axes is not None:
             file_handle[self.path].attrs['axes'] = self._axes
@@ -84,10 +96,12 @@ class _Stack:
             raise RuntimeError('Cannot append data to the stack entry at {}. The previous slice has not been written '
                                'yet.'.format(self.path))
 
-        if type(data) != self._data_type:
+        data_type = _assign_data_type(data)
+
+        if data_type != self._data_type:
             raise RuntimeError('The type of the input data does not match what is already present in the stack.')
 
-        if isinstance(data, (str, int, float)):
+        if isinstance(data, (bytes, int, float)):
             curr_data_shape = (1,)
         else:
             curr_data_shape = data.shape
@@ -109,8 +123,9 @@ class _Stack:
 
 
 def _validate_data(data):
-    if not isinstance(data, (str, int, float, numpy.ndarray)):
-        raise RuntimeError('The CXI Writer only accepts numpy objects, numbers and strings.')
+
+    if not isinstance(data, (bytes, int, float, numpy.ndarray)):
+        raise RuntimeError('The CXI Writer only accepts numpy objects, numbers and ascii strings.')
 
 
 class CXIWriter:
@@ -234,10 +249,10 @@ class CXIWriter:
             
             path (str): path in the hdf5 file where the stack will be written.
             
-            initial_data (Union[numpy.ndarray, str, int, float]: initial entry in the stack. It gets written to the 
+            initial_data (Union[numpy.ndarray, bytes, int, float]: initial entry in the stack. It gets written to the 
             stack as slice 0. Its characteristics are used to validate all data subsequently appended to the stack.
             
-            axes (str): the 'axes' attribute for the stack, as defined by the CXIDB file format.
+            axes (bytes): the 'axes' attribute for the stack, as defined by the CXIDB file format.
             
             compression (Union[None, bool,str]): compression parameter for the stack. This parameters works in the same
             way as the normal compression parameter from h5py. The default value of this parameter is True.
@@ -280,7 +295,7 @@ class CXIWriter:
         
             path (str): path in the hdf5 file where the entry will be written.
             
-            data (Union: numpy.ndarray, str, int, float): data to write
+            data (Union[numpy.ndarray, bytes, int, float]): data to write
             
             overwrite (bool): if set to True, an entry already existing at the same location will be overwritten. If set
             to False, an attempt to overwrite an entry will raise an error.
@@ -363,7 +378,7 @@ class CXIWriter:
                 raise RuntimeError('Cannot create the link. An entry already exists at the specified path.')
 
         try:
-            link_target = self._fh[path]
+            link_target = self._fh[group]
         except KeyError:
             raise RuntimeError('Cannot create the link. The group to which the link points does not exist.')
 
@@ -405,7 +420,7 @@ class CXIWriter:
             
             name (str): stack name, defining the stack to which the data will be appended.
             
-            data (Union: numpy.ndarray, str, int, float): data to write. The data will be validated against the type
+            data (Union[numpy.ndarray, bytes, int, float]: data to write. The data will be validated against the type
             and size of previous entries in the stack.
         """
 
diff --git a/doc/build/doctrees/cfelpyutils.doctree b/doc/build/doctrees/cfelpyutils.doctree
index ae9ba9df5c4e2d3ac777db7a9cf2d7936b0bafc2..a41051f8809eafee804847961801c5089599379d 100644
GIT binary patch
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diff --git a/doc/build/html/cfelpyutils.html b/doc/build/html/cfelpyutils.html
index 7e5d627..7d2a7f3 100644
--- a/doc/build/html/cfelpyutils.html
+++ b/doc/build/html/cfelpyutils.html
@@ -193,9 +193,9 @@ the stack.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>name</strong> (<em>str</em>) &#8211; stack name.</li>
 <li><strong>path</strong> (<em>str</em>) &#8211; path in the hdf5 file where the stack will be written.</li>
-<li><strong></strong><strong>(</strong><strong>Union</strong><strong>[</strong><strong>numpy.ndarray</strong><strong>, </strong><strong>str</strong><strong>, </strong><strong>int</strong><strong>, </strong><strong>float</strong><strong>]</strong><strong></strong> (<em>initial_data</em>) &#8211; initial entry in the stack. It gets written to the</li>
+<li><strong></strong><strong>(</strong><strong>Union</strong><strong>[</strong><strong>numpy.ndarray</strong><strong>, </strong><strong>bytes</strong><strong>, </strong><strong>int</strong><strong>, </strong><strong>float</strong><strong>]</strong><strong></strong> (<em>initial_data</em>) &#8211; initial entry in the stack. It gets written to the</li>
 <li><strong>as slice 0. Its characteristics are used to validate all data subsequently appended to the stack.</strong> (<em>stack</em>) &#8211; </li>
-<li><strong>axes</strong> (<em>str</em>) &#8211; the &#8216;axes&#8217; attribute for the stack, as defined by the CXIDB file format.</li>
+<li><strong>axes</strong> (<em>bytes</em>) &#8211; the &#8216;axes&#8217; attribute for the stack, as defined by the CXIDB file format.</li>
 <li><strong>compression</strong> (<em>Union</em><em>[</em><em>None</em><em>, </em><em>bool</em><em>,</em><em>str</em><em>]</em><em></em>) &#8211; compression parameter for the stack. This parameters works in the same</li>
 <li><strong>as the normal compression parameter from h5py. The default value of this parameter is True.</strong> (<em>way</em>) &#8211; </li>
 <li><strong>chunk_size</strong> (<em>Union</em><em>[</em><em>None</em><em>, </em><em>tuple</em><em>]</em><em></em>) &#8211; HDF5 chuck size for the stack. If this parameter is set to None, the</li>
@@ -223,7 +223,7 @@ the write_slice_and_increment.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>name</strong> (<em>str</em>) &#8211; stack name, defining the stack to which the data will be appended.</li>
-<li><strong></strong><strong>(</strong><strong>Union</strong> (<em>data</em>) &#8211; numpy.ndarray, str, int, float): data to write. The data will be validated against the type</li>
+<li><strong></strong><strong>(</strong><strong>Union</strong><strong>[</strong><strong>numpy.ndarray</strong><strong>, </strong><strong>bytes</strong><strong>, </strong><strong>int</strong><strong>, </strong><strong>float</strong><strong>]</strong><strong></strong> (<em>data</em>) &#8211; data to write. The data will be validated against the type</li>
 <li><strong>size of previous entries in the stack.</strong> (<em>and</em>) &#8211; </li>
 </ul>
 </td>
@@ -359,7 +359,7 @@ operations (for example, creating a link).</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>name</strong> (<em>str</em>) &#8211; entry name</li>
 <li><strong>path</strong> (<em>str</em>) &#8211; path in the hdf5 file where the entry will be written.</li>
-<li><strong></strong><strong>(</strong><strong>Union</strong> (<em>data</em>) &#8211; numpy.ndarray, str, int, float): data to write</li>
+<li><strong>data</strong> (<em>Union</em><em>[</em><em>numpy.ndarray</em><em>, </em><em>bytes</em><em>, </em><em>int</em><em>, </em><em>float</em><em>]</em><em></em>) &#8211; data to write</li>
 <li><strong>overwrite</strong> (<em>bool</em>) &#8211; if set to True, an entry already existing at the same location will be overwritten. If set</li>
 <li><strong>False</strong><strong>, </strong><strong>an attempt to overwrite an entry will raise an error.</strong> (<em>to</em>) &#8211; </li>
 </ul>
diff --git a/doc/build/html/searchindex.js b/doc/build/html/searchindex.js
index 5f77a38..113258d 100644
--- a/doc/build/html/searchindex.js
+++ b/doc/build/html/searchindex.js
@@ -1 +1 @@
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