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Commit 4d5fd388 authored by Valerio Mariani's avatar Valerio Mariani
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Fixed some bugs, added some checks and documentation

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cfel_cxi.py
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− 14
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...@@ -25,20 +25,29 @@ from __future__ import division ...@@ -25,20 +25,29 @@ from __future__ import division
from __future__ import print_function from __future__ import print_function
from __future__ import unicode_literals from __future__ import unicode_literals
from builtins import str
from collections import namedtuple from collections import namedtuple
import h5py import h5py
import numpy
_CXISimpleEntry = namedtuple('SimpleEntry', ['path', 'data', 'overwrite']) _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: class _Stack:
def __init__(self, path, data, axes, compression, chunk_size): 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,) self._data_shape = (1,)
else: else:
self._data_shape = data.shape self._data_shape = data.shape
...@@ -63,9 +72,12 @@ class _Stack: ...@@ -63,9 +72,12 @@ class _Stack:
def write_initial_slice(self, file_handle, max_num_slices): 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,
dtype = self._data_type,
maxshape=(max_num_slices,) + self._data_shape, maxshape=(max_num_slices,) + self._data_shape,
compression=self._compression, chunks=self._chunk_size) 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: if self._axes is not None:
file_handle[self.path].attrs['axes'] = self._axes file_handle[self.path].attrs['axes'] = self._axes
...@@ -84,10 +96,12 @@ class _Stack: ...@@ -84,10 +96,12 @@ class _Stack:
raise RuntimeError('Cannot append data to the stack entry at {}. The previous slice has not been written ' 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: 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.') 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,) curr_data_shape = (1,)
else: else:
curr_data_shape = data.shape curr_data_shape = data.shape
...@@ -109,8 +123,9 @@ class _Stack: ...@@ -109,8 +123,9 @@ class _Stack:
def _validate_data(data): 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: class CXIWriter:
...@@ -234,10 +249,10 @@ class CXIWriter: ...@@ -234,10 +249,10 @@ class CXIWriter:
path (str): path in the hdf5 file where the stack will be written. 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. 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 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. way as the normal compression parameter from h5py. The default value of this parameter is True.
...@@ -280,7 +295,7 @@ class CXIWriter: ...@@ -280,7 +295,7 @@ class CXIWriter:
path (str): path in the hdf5 file where the entry will be written. 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 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. to False, an attempt to overwrite an entry will raise an error.
...@@ -363,7 +378,7 @@ class CXIWriter: ...@@ -363,7 +378,7 @@ class CXIWriter:
raise RuntimeError('Cannot create the link. An entry already exists at the specified path.') raise RuntimeError('Cannot create the link. An entry already exists at the specified path.')
try: try:
link_target = self._fh[path] link_target = self._fh[group]
except KeyError: except KeyError:
raise RuntimeError('Cannot create the link. The group to which the link points does not exist.') raise RuntimeError('Cannot create the link. The group to which the link points does not exist.')
...@@ -405,7 +420,7 @@ class CXIWriter: ...@@ -405,7 +420,7 @@ class CXIWriter:
name (str): stack name, defining the stack to which the data will be appended. 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. and size of previous entries in the stack.
""" """
......
doc/build/doctrees/cfelpyutils.doctree
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doc/build/doctrees/environment.pickle
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doc/build/html/cfelpyutils.html
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...@@ -193,9 +193,9 @@ the stack.</p> ...@@ -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"> <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>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>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>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>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>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>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> ...@@ -223,7 +223,7 @@ the write_slice_and_increment.</p>
<tbody valign="top"> <tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> <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>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> <li><strong>size of previous entries in the stack.</strong> (<em>and</em>) &#8211; </li>
</ul> </ul>
</td> </td>
...@@ -359,7 +359,7 @@ operations (for example, creating a link).</p> ...@@ -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"> <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>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>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>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> <li><strong>False</strong><strong>, </strong><strong>an attempt to overwrite an entry will raise an error.</strong> (<em>to</em>) &#8211; </li>
</ul> </ul>
......
doc/build/html/searchindex.js
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