diff --git a/cfel_cxi.py b/cfel_cxi.py
index 7eb26dd718464f6582c3008d4d1de480b5b27785..9e196d3cbeaab4bf666dade7360585861a45b0e9 100644
--- a/cfel_cxi.py
+++ b/cfel_cxi.py
@@ -29,7 +29,6 @@ from builtins import str
from collections import namedtuple
import h5py
-import numpy
_CXISimpleEntry = namedtuple('SimpleEntry', ['path', 'data', 'overwrite'])
@@ -45,7 +44,7 @@ class _Stack:
self._data_shape = data.shape
self._data_to_write = data
- self._path = path
+ self.path = path
self._axes = axes
self._compression = compression
@@ -61,28 +60,21 @@ class _Stack:
else:
return False
- def is_there_data_to_write(self):
-
- if self._data_to_write is not None:
- return True
- else:
- return False
-
def write_initial_slice(self, file_handle, max_num_slices):
- file_handle.create_dataset(self._path, shape=(max_num_slices,) + self._data_shape,
+ file_handle.create_dataset(self.path, shape=(max_num_slices,) + self._data_shape,
maxshape=(max_num_slices,) + self._data_shape,
- compression = self._compression, chunks=self._chunk_size)
- file_handle[self._path][0] = self._data_to_write
+ compression=self._compression, chunks=self._chunk_size)
+ file_handle[self.path][0] = self._data_to_write
if self._axes is not None:
- file_handle[self._path].attrs['axes'] = self._axes
+ file_handle[self.path].attrs['axes'] = self._axes
self._data_to_write = None
def write_slice(self, file_handle, curr_slice):
- file_handle[self._path][curr_slice] = self._data_to_write
+ file_handle[self.path][curr_slice] = self._data_to_write
self._data_to_write = None
@@ -90,7 +82,7 @@ class _Stack:
if self._data_to_write is not None:
raise RuntimeError('Cannot append data to the stack entry at {}. The previous slice has not been written '
- 'yet.'.format(self._path))
+ 'yet.'.format(self.path))
if type(data) != self._data_type:
raise RuntimeError('The type of the input data does not match what is already present in the stack.')
@@ -109,11 +101,11 @@ class _Stack:
if self._data_to_write is not None:
raise RuntimeError('Cannot finalize the stack at {}, there is data waiting to be '
- 'written.'.format(self._path))
+ 'written.'.format(self.path))
final_size = curr_slice
- file_handle[self._path].resize((final_size,) + self._data_shape)
+ file_handle[self.path].resize((final_size,) + self._data_shape)
def _validate_data(data):
@@ -160,8 +152,8 @@ class CXIWriter:
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.write_simple_entry('detectorname1', '/entry_1/detector_1/name', 'FrontCSPAD')
+ f2.write_simple_entry('detectorname2', '/entry_1/detector_1/name', 'BackCSPAD')
f1.initialize_stacks()
f2.initialize_stacks()
@@ -181,6 +173,9 @@ class CXIWriter:
f1.write_stack_slice_and_increment()
f2.write_stack_slice_and_increment()
+ f1.create_link('detectorname1', '/name')
+ f2.create_link('detectorname2', '/name')
+
f1.close_file()
f2.close_file()
"""
@@ -199,6 +194,7 @@ class CXIWriter:
self._cxi_stacks = {}
self._pending_simple_entries = []
+ self._simple_entries = {}
self._intialized = False
self._curr_slice = 0
self._max_num_slices = max_num_slices
@@ -256,6 +252,9 @@ class CXIWriter:
_validate_data(initial_data)
+ if name in self._cxi_stacks:
+ raise RuntimeError('A stack with the provided name already exists.')
+
if self._initialized is True:
raise RuntimeError('Adding stacks to the writer is not possible after initialization.')
@@ -268,14 +267,17 @@ class CXIWriter:
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):
+ def write_simple_entry(self, name, path, data, overwrite=False):
"""Writes a simple, non-stack entry in the file.
Writes a simple, non-stack entry in the file, at the specified path. A simple entry can be written at all times,
- before or after the stack initialization.
+ before or after the stack initialization. THe user must provide a name that identifies the entry for further
+ operations (for example, creating a link).
Args:
+ name (str): entry name
+
path (str): path in the hdf5 file where the entry will be written.
data (Union: numpy.ndarray, str, int, float): data to write
@@ -286,6 +288,15 @@ class CXIWriter:
_validate_data(data)
+ if name in self._simple_entries:
+ raise RuntimeError('An entry with the provided name already exists.')
+
+ if path in self._fh:
+ if overwrite is True:
+ del (self._fh[path])
+ else:
+ raise RuntimeError('Cannot create the the entry. An entry already exists at the specified path.')
+
new_entry = _CXISimpleEntry(path, data, overwrite)
if self._initialized is not True:
@@ -293,6 +304,41 @@ class CXIWriter:
else:
self._write_simple_entry(new_entry)
+ self._simple_entries[name] = new_entry
+
+ def create_link(self, name, path, overwrite=False):
+ """Creates a link to a stack or entry.
+
+ Creates a link in the file, at the path specified, pointing to the stack or the entry identified by the
+ provided name. If a link or entry already exists at the specified path, it is deleted and replaced only if the
+ value of the overwrite parameter is True.
+
+ Args:
+
+ name (str): name of the stack or entry to which the link points.
+
+ path (str): path in the hdf5 where the link is created.
+
+ 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.
+ """
+
+ if path in self._fh:
+ if overwrite is True:
+ del (self._fh[path])
+ else:
+ raise RuntimeError('Cannot create the link. An entry already exists at the specified path.')
+
+ try:
+ link_target = self._fh[self._cxi_stacks[name].path]
+ except KeyError:
+ try:
+ link_target = self._fh[self._simple_entries[name].path]
+ except:
+ raise RuntimeError('Cannot find an entry or stack with the proveded name.')
+
+ self._fh[path] = link_target
+
def initialize_stacks(self):
"""Initializes the stacks.
@@ -404,3 +450,48 @@ class CXIWriter:
self._fh.close()
self._file_is_open = False
+
+
+if __name__ == '__main__':
+ import numpy
+
+ 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('detectorname1', '/entry_1/detector_1/name', 'FrontCSPAD')
+ f2.write_simple_entry('detectorname2', '/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.create_link('detectorname1', '/name')
+ f2.create_link('detectorname2', '/name')
+
+ f1.close_file()
+ f2.close_file()
diff --git a/doc/build/doctrees/cfelpyutils.doctree b/doc/build/doctrees/cfelpyutils.doctree
index f7fcad63c139cbbabdebc2add4aa5841893c6a9f..447fe6ec10ac30061864de9f704d06aa8556093d 100644
Binary files a/doc/build/doctrees/cfelpyutils.doctree and b/doc/build/doctrees/cfelpyutils.doctree differ
diff --git a/doc/build/doctrees/environment.pickle b/doc/build/doctrees/environment.pickle
index b25b8954d67843b8eee04b36c0bfc7de84be7e54..fa918e092bdeb8c07df61a429b0460a5cb092da8 100644
Binary files a/doc/build/doctrees/environment.pickle and b/doc/build/doctrees/environment.pickle differ
diff --git a/doc/build/html/cfelpyutils.html b/doc/build/html/cfelpyutils.html
index 1c0160ae1968dfef63b6ea45adb82712ef4c3c99..fba5fea547f35b2643ff95e7ac1a28fa7239c9be 100644
--- a/doc/build/html/cfelpyutils.html
+++ b/doc/build/html/cfelpyutils.html
@@ -159,8 +159,8 @@ f2 = CXIWriter(‘test2.h5’, )</p>
</dl>
<p>f1.add_stack_to_writer(‘counter1’, ‘/entry_1/detector_1/count’, c1)
f2.add_stack_to_writer(‘counter2’, ‘/entry_1/detector_1/count’, c2)</p>
-<p>f1.write_simple_entry(‘/entry_1/detector_1/name’, ‘FrontCSPAD’)
-f2.write_simple_entry(‘/entry_1/detector_1/name’, ‘BackCSPAD’)</p>
+<p>f1.write_simple_entry(‘detectorname1’, ‘/entry_1/detector_1/name’, ‘FrontCSPAD’)
+f2.write_simple_entry(‘detectorname2’, ‘/entry_1/detector_1/name’, ‘BackCSPAD’)</p>
<p>f1.initialize_stacks()
f2.initialize_stacks()</p>
<p>a = numpy.random.rand(2, 2)
@@ -173,6 +173,8 @@ f2.append_data_to_stack(‘detector2’, b)</p>
f2.append_data_to_stack(‘counter2’, c2)</p>
<p>f1.write_stack_slice_and_increment()
f2.write_stack_slice_and_increment()</p>
+<p>f1.create_link(‘detectorname1’, ‘/name’)
+f2.create_link(‘detectorname2’, ‘/name’)</p>
<p>f1.close_file()
f2.close_file()</p>
<dl class="method">
@@ -237,6 +239,29 @@ the write_slice_and_increment.</p>
<p>Closes the file for writing, ending all writing operations.</p>
</dd></dl>
+<dl class="method">
+<dt id="cfelpyutils.cfel_cxi.CXIWriter.create_link">
+<code class="descname">create_link</code><span class="sig-paren">(</span><em>name</em>, <em>path</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfel_cxi.CXIWriter.create_link" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates a link to a stack or entry.</p>
+<p>Creates a link in the file, at the path specified, pointing to the stack or the entry identified by the
+provided name. If a link or entry already exists at the specified path, it is deleted and replaced only if the
+value of the overwrite parameter is True.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<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>) – name of the stack or entry to which the link points.</li>
+<li><strong>path</strong> (<em>str</em>) – path in the hdf5 where the link is created.</li>
+<li><strong>overwrite</strong> (<em>bool</em>) – 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>) – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="method">
<dt id="cfelpyutils.cfel_cxi.CXIWriter.get_file_handle">
<code class="descname">get_file_handle</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfel_cxi.CXIWriter.get_file_handle" title="Permalink to this definition">¶</a></dt>
@@ -265,15 +290,17 @@ stacks can be added to the CXI Writer after initialization.</p>
<dl class="method">
<dt id="cfelpyutils.cfel_cxi.CXIWriter.write_simple_entry">
-<code class="descname">write_simple_entry</code><span class="sig-paren">(</span><em>path</em>, <em>data</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfel_cxi.CXIWriter.write_simple_entry" title="Permalink to this definition">¶</a></dt>
+<code class="descname">write_simple_entry</code><span class="sig-paren">(</span><em>name</em>, <em>path</em>, <em>data</em>, <em>overwrite=False</em><span class="sig-paren">)</span><a class="headerlink" href="#cfelpyutils.cfel_cxi.CXIWriter.write_simple_entry" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes a simple, non-stack entry in the file.</p>
<p>Writes a simple, non-stack entry in the file, at the specified path. A simple entry can be written at all times,
-before or after the stack initialization.</p>
+before or after the stack initialization. THe user must provide a name that identifies the entry for further
+operations (for example, creating a link).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<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>) – entry name</li>
<li><strong>path</strong> (<em>str</em>) – path in the hdf5 file where the entry will be written.</li>
<li><strong></strong><strong>(</strong><strong>Union</strong> (<em>data</em>) – numpy.ndarray, str, int, float): data to write</li>
<li><strong>overwrite</strong> (<em>bool</em>) – if set to True, an entry already existing at the same location will be overwritten. If set</li>
diff --git a/doc/build/html/genindex.html b/doc/build/html/genindex.html
index 47fda0ca21f87be7545c690be6489ed021546e47..32f0bac53fa8f703cebe2a318226b439f18be072 100644
--- a/doc/build/html/genindex.html
+++ b/doc/build/html/genindex.html
@@ -123,6 +123,8 @@
<li><a href="cfelpyutils.html#module-cfelpyutils.cfel_psana">cfelpyutils.cfel_psana (module)</a>
</li>
<li><a href="cfelpyutils.html#cfelpyutils.cfel_cxi.CXIWriter.close_file">close_file() (cfelpyutils.cfel_cxi.CXIWriter method)</a>
+</li>
+ <li><a href="cfelpyutils.html#cfelpyutils.cfel_cxi.CXIWriter.create_link">create_link() (cfelpyutils.cfel_cxi.CXIWriter method)</a>
</li>
<li><a href="cfelpyutils.html#cfelpyutils.cfel_cxi.CXIWriter">CXIWriter (class in cfelpyutils.cfel_cxi)</a>
</li>
diff --git a/doc/build/html/objects.inv b/doc/build/html/objects.inv
index 6de1c8cb9adcb25cc66471633eab7df221f4884f..4f56f0849919d1db670dbdd65f15d86fa81f0280 100644
Binary files a/doc/build/html/objects.inv and b/doc/build/html/objects.inv differ
diff --git a/doc/build/html/searchindex.js b/doc/build/html/searchindex.js
index 6de89ba88616fb47ba0b9f042813f1ba60bb5e1a..6589a4cede487aa54871ec8e9459008d42c24759 100644
--- a/doc/build/html/searchindex.js
+++ b/doc/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["cfelpyutils","index","modules"],envversion:51,filenames:["cfelpyutils.rst","index.rst","modules.rst"],objects:{"":{cfelpyutils:[0,0,0,"-"]},"cfelpyutils.cfel_crystfel":{load_crystfel_geometry:[0,1,1,""]},"cfelpyutils.cfel_cxi":{CXIWriter:[0,2,1,""]},"cfelpyutils.cfel_cxi.CXIWriter":{add_stack_to_writer:[0,3,1,""],append_data_to_stack:[0,3,1,""],close_file:[0,3,1,""],get_file_handle:[0,3,1,""],initialize_stacks:[0,3,1,""],write_simple_entry:[0,3,1,""],write_stack_slice_and_increment:[0,3,1,""]},"cfelpyutils.cfel_fabio":{read_cbf_from_stream:[0,1,1,""]},"cfelpyutils.cfel_geom":{apply_geometry_from_file:[0,1,1,""],apply_geometry_from_pixel_maps:[0,1,1,""],pixel_maps_for_image_view:[0,1,1,""],pixel_maps_from_geometry_file:[0,1,1,""]},"cfelpyutils.cfel_hdf5":{load_nparray_from_hdf5_file:[0,1,1,""]},"cfelpyutils.cfel_optarg":{parse_parameters:[0,1,1,""]},"cfelpyutils.cfel_psana":{dirname_from_source_runs:[0,1,1,""],psana_event_inspection:[0,1,1,""],psana_obj_from_string:[0,1,1,""]},cfelpyutils:{cfel_crystfel:[0,0,0,"-"],cfel_cxi:[0,0,0,"-"],cfel_fabio:[0,0,0,"-"],cfel_geom:[0,0,0,"-"],cfel_hdf5:[0,0,0,"-"],cfel_optarg:[0,0,0,"-"],cfel_psana:[0,0,0,"-"]}},objnames:{"0":["py","module","Python 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