Added compression and chunk size support to the CXI Writer

cfel_cxi.py

@@ -35,7 +35,7 @@ _CXISimpleEntry = namedtuple('SimpleEntry', ['path', 'data', 'overwrite'])
 
 
 class _Stack:
-    def __init__(self, path, data, axes):
+    def __init__(self, path, data, axes, compression, chunk_size):
 
         self._data_type = type(data)
 
@@ -47,6 +47,12 @@ class _Stack:
         self._data_to_write = data
         self._path = path
         self._axes = axes
+        self._compression = compression
+
+        if chunk_size is None:
+            self._chunk_size = (1,) + self._data_shape
+        else:
+            self._chunk_size = chunk_size
 
     def is_there_data_to_write(self):
 
@@ -59,7 +65,7 @@ class _Stack:
 
         file_handle.create_dataset(self._path, shape=(max_num_slices,) + self._data_shape,
                                    maxshape=(max_num_slices,) + self._data_shape,
-                                   chunks=(1,) + self._data_shape)
+                                   compression = self._compression, chunks=self._chunk_size)
         file_handle[self._path][0] = self._data_to_write
 
         if self._axes is not None:
@@ -133,45 +139,43 @@ class CXIWriter:
     
     Example of usage of the stack API:
     
-        c1 = 0
-        c2 = 0
-    
-        f1 = CXIWriter('/data/test1.h5', )
-        f2 = CXIWriter('/data/test2.h5', )
-    
-        f1.add_stack_to_writer('detector1', '/entry_1/detector_1/data', numpy.random.rand(2, 2),
-                               'frame:y:x')
-        f2.add_stack_to_writer('detector2', '/entry_1/detector_1/data', numpy.random.rand(3, 2))
-                               'frame:y:x')
-    
-        f1.add_stack_to_writer('counter1', '/entry_1/detector_1/count', c1)
-        f2.add_stack_to_writer('counter2', '/entry_1/detector_1/count', c2)
-    
-        f1.write_simple_entry('/entry_1/detector_1/name', 'FrontCSPAD')
-        f2.write_simple_entry('/entry_1/detector_1/name', 'BackCSPAD')
-    
-        f1.initialize_stacks()
-        f2.initialize_stacks()
-    
-        for i in range(1, 60):
-            print('Writing slice:', i)
-            a = numpy.random.rand(2, 2)
-            b = numpy.random.rand(3, 2)
-    
-            c1 += 1
-            c2 += 2
-    
-            f1.append_data_to_stack('detector1', a)
-            f2.append_data_to_stack('detector2', b)
-    
-            f1.append_data_to_stack('counter1', c1)
-            f2.append_data_to_stack('counter2', c2)
-    
-            f1.write_stack_slice_and_increment()
-            f2.write_stack_slice_and_increment()
-    
-        f1.close_file()
-        f2.close_file()    
+    c1 = 0
+    c2 = 0
+
+    f1 = CXIWriter('test1.h5', )
+    f2 = CXIWriter('test2.h5', )
+
+    f1.add_stack_to_writer('detector1', '/entry_1/detector_1/data', numpy.random.rand(2, 2),
+                           'frame:y:x')
+    f2.add_stack_to_writer('detector2', '/entry_1/detector_1/data', numpy.random.rand(3, 2),
+                           'frame:y:x', compression=False, chunk_size=(1,3,2))
+
+    f1.add_stack_to_writer('counter1', '/entry_1/detector_1/count', c1)
+    f2.add_stack_to_writer('counter2', '/entry_1/detector_1/count', c2)
+
+    f1.write_simple_entry('/entry_1/detector_1/name', 'FrontCSPAD')
+    f2.write_simple_entry('/entry_1/detector_1/name', 'BackCSPAD')
+
+    f1.initialize_stacks()
+    f2.initialize_stacks()
+
+    a = numpy.random.rand(2, 2)
+    b = numpy.random.rand(3, 2)
+
+    c1 += 1
+    c2 += 2
+
+    f1.append_data_to_stack('detector1', a)
+    f2.append_data_to_stack('detector2', b)
+
+    f1.append_data_to_stack('counter1', c1)
+    f2.append_data_to_stack('counter2', c2)
+
+    f1.write_stack_slice_and_increment()
+    f2.write_stack_slice_and_increment()
+
+    f1.close_file()
+    f2.close_file()
     """
 
     def __init__(self, filename, max_num_slices=5000):
@@ -211,7 +215,8 @@ class CXIWriter:
 
         self._fh.create_dataset(entry.path, data=entry.data)
 
-    def add_stack_to_writer(self, name, path, initial_data, axes=None, overwrite=True):
+    def add_stack_to_writer(self, name, path, initial_data, axes=None, compression=True, chunk_size=None,
+                            overwrite=True):
         """Adds a new stack to the file.
         
         Adds a new stack to the CXI Writer instance. The user must provide a name for the stack, that will identify
@@ -226,11 +231,18 @@ 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, str, 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.
             
+            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.
+            
+            chunk_size (Union[None, tuple]): HDF5 chuck size for the stack. If this parameter is set to None, the
+            CXI writer will compute a chuck size automatically (this is the default behavior). Otherwise, the writer 
+            will use the provided tuple to set the chunk size.
+            
             overwrite (bool): if set to True, a stack already existing at the same location will be overwritten. If set
             to False, an attempt to overwrite a stack will raise an error.
         """
@@ -246,7 +258,7 @@ class CXIWriter:
             else:
                 raise RuntimeError('Cannot write the entry. Data is already present at the specified path.')
 
-        new_stack = _Stack(path, initial_data, axes)
+        new_stack = _Stack(path, initial_data, axes, compression, chunk_size)
         self._cxi_stacks[name] = new_stack
 
     def write_simple_entry(self, path, data, overwrite=False):

doc/build/html/_sources/cfelpyutils.rst.txt

+cfelpyutils package
+===================
+
+Submodules
+----------
+
+cfelpyutils.cfel_crystfel module
+--------------------------------
+
+.. automodule:: cfelpyutils.cfel_crystfel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cfelpyutils.cfel_cxi module
+---------------------------
+
+.. automodule:: cfelpyutils.cfel_cxi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cfelpyutils.cfel_fabio module
+-----------------------------
+
+.. automodule:: cfelpyutils.cfel_fabio
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cfelpyutils.cfel_geom module
+----------------------------
+
+.. automodule:: cfelpyutils.cfel_geom
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cfelpyutils.cfel_hdf5 module
+----------------------------
+
+.. automodule:: cfelpyutils.cfel_hdf5
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cfelpyutils.cfel_optarg module
+------------------------------
+
+.. automodule:: cfelpyutils.cfel_optarg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+cfelpyutils.cfel_psana module
+-----------------------------
+
+.. automodule:: cfelpyutils.cfel_psana
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: cfelpyutils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/build/html/_sources/index.rst.txt

+.. cfelpyutils documentation master file, created by
+   sphinx-quickstart on Wed Mar 30 11:47:49 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to cfelpyutils's documentation!
+=======================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

doc/build/html/_sources/modules.rst.txt

+cfelpyutils
+===========
+
+.. toctree::
+   :maxdepth: 4
+
+   cfelpyutils

doc/build/html/cfelpyutils.html

@@ -147,16 +147,15 @@ number_of_entries specified during instantiation.</p>
 course that the file is open). Entries and stacks will general never be overwritten unless the overwrite parameter
 is set to True.</p>
 <p>Example of usage of the stack API:</p>
-<blockquote>
-<div><p>c1 = 0
+<p>c1 = 0
 c2 = 0</p>
-<p>f1 = CXIWriter(&#8216;/data/test1.h5&#8217;, )
-f2 = CXIWriter(&#8216;/data/test2.h5&#8217;, )</p>
+<p>f1 = CXIWriter(&#8216;test1.h5&#8217;, )
+f2 = CXIWriter(&#8216;test2.h5&#8217;, )</p>
 <dl class="docutils">
 <dt>f1.add_stack_to_writer(&#8216;detector1&#8217;, &#8216;/entry_1/detector_1/data&#8217;, numpy.random.rand(2, 2),</dt>
 <dd>&#8216;frame:y:x&#8217;)</dd>
-<dt>f2.add_stack_to_writer(&#8216;detector2&#8217;, &#8216;/entry_1/detector_1/data&#8217;, numpy.random.rand(3, 2))</dt>
-<dd>&#8216;frame:y:x&#8217;)</dd>
+<dt>f2.add_stack_to_writer(&#8216;detector2&#8217;, &#8216;/entry_1/detector_1/data&#8217;, numpy.random.rand(3, 2),</dt>
+<dd>&#8216;frame:y:x&#8217;, compression=False, chunk_size=(1,3,2))</dd>
 </dl>
 <p>f1.add_stack_to_writer(&#8216;counter1&#8217;, &#8216;/entry_1/detector_1/count&#8217;, c1)
 f2.add_stack_to_writer(&#8216;counter2&#8217;, &#8216;/entry_1/detector_1/count&#8217;, c2)</p>
@@ -164,10 +163,7 @@ f2.add_stack_to_writer(&#8216;counter2&#8217;, &#8216;/entry_1/detector_1/count&
 f2.write_simple_entry(&#8216;/entry_1/detector_1/name&#8217;, &#8216;BackCSPAD&#8217;)</p>
 <p>f1.initialize_stacks()
 f2.initialize_stacks()</p>
-<dl class="docutils">
-<dt>for i in range(1, 60):</dt>
-<dd><p class="first">print(&#8216;Writing slice:&#8217;, i)
-a = numpy.random.rand(2, 2)
+<p>a = numpy.random.rand(2, 2)
 b = numpy.random.rand(3, 2)</p>
 <p>c1 += 1
 c2 += 2</p>
@@ -175,16 +171,13 @@ c2 += 2</p>
 f2.append_data_to_stack(&#8216;detector2&#8217;, b)</p>
 <p>f1.append_data_to_stack(&#8216;counter1&#8217;, c1)
 f2.append_data_to_stack(&#8216;counter2&#8217;, c2)</p>
-<p class="last">f1.write_stack_slice_and_increment()
+<p>f1.write_stack_slice_and_increment()
 f2.write_stack_slice_and_increment()</p>
-</dd>
-</dl>
 <p>f1.close_file()
 f2.close_file()</p>
-</div></blockquote>
 <dl class="method">
 <dt id="cfelpyutils.cfel_cxi.CXIWriter.add_stack_to_writer">
-<code class="descname">add_stack_to_writer</code><span class="sig-paren">(</span><em>name</em>, <em>path</em>, <em>initial_data</em>, <em>axes=None</em>, <em>overwrite=True</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfel_cxi.CXIWriter.add_stack_to_writer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_stack_to_writer</code><span class="sig-paren">(</span><em>name</em>, <em>path</em>, <em>initial_data</em>, <em>axes=None</em>, <em>compression=True</em>, <em>chunk_size=None</em>, <em>overwrite=True</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfel_cxi.CXIWriter.add_stack_to_writer" title="Permalink to this definition">¶</a></dt>
 <dd><p>Adds a new stack to the file.</p>
 <p>Adds a new stack to the CXI Writer instance. The user must provide a name for the stack, that will identify
 the stack in all subsequents operations. The user must also provide the data that will be written as the
@@ -198,9 +191,14 @@ 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> (<em>initial_data</em>) &#8211; numpy.ndarray, str, int, float): 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>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>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>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>
+<li><strong>writer will compute a chuck size automatically</strong> (<em>CXI</em>) &#8211; </li>
+<li><strong>use the provided tuple to set the chunk size.</strong> (<em>will</em>) &#8211; </li>
 <li><strong>overwrite</strong> (<em>bool</em>) &#8211; if set to True, a stack already existing at the same location will be overwritten. If set</li>
 <li><strong>False</strong><strong>, </strong><strong>an attempt to overwrite a stack will raise an error.</strong> (<em>to</em>) &#8211; </li>
 </ul>

doc/build/html/searchindex.js

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