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‎CHANGELOG.rst‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,11 @@ This document records all notable changes to
88
This project adheres to `PEP 440 -- Version Identification
99
and Dependency Specification <https://www.python.org/dev/peps/pep-0440/>`_.
1010

11+
0.4.4 (22-10-13)
12+
-----------------
13+
- Bug fixes (x- and y-axis vectors failing to generate with imported HDF5 files)
14+
- Minor tweaks and improvements
15+
1116
0.4.3 (22-08-03)
1217
----------------
1318
- Spectrum and Hsi now moved to **data.spectra**. **This could break your fork if you have custom code.**

‎crikit/CRIkitUI.py‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -893,9 +893,8 @@ def fileOpenSuccess(self, success):
893893
if self.ui.actionUndo_Backup_Enabled.isChecked():
894894
try:
895895
_BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
896-
except Exception as e:
897-
_traceback.print_exc(limit=1)
898-
print(e)
896+
except Exception:
897+
_traceback.print_exc()
899898
print('Error in pickle backup (Undo functionality)')
900899
else:
901900
self.bcpre.backed_up()

‎crikit/__init__.py‎

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@@ -14,4 +14,4 @@
1414
* Charles H. Camp Jr. <[email protected]>
1515
"""
1616

17-
__version__ = '0.4.3'
17+
__version__ = '0.4.4'

‎crikit/io/hdf5.py‎

Lines changed: 6 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,8 @@
2121
__all__ = ['hdf_import_data', 'hdf_import_data_macroraster']
2222

2323

24-
def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None):
24+
def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None,
25+
interp_kind_spatial='linear', interp_kind_spectral='linear'):
2526
"""
2627
Import dataset(s) from HDF file with each dset being a single line scan.
2728
@@ -107,10 +108,11 @@ def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, c
107108
all_xs.extend(curr_x_vec.tolist())
108109
all_ys.extend([curr_y_pos])
109110

110-
intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind='linear')
111+
intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind=interp_kind_spatial)
111112

112113
int_fcn_intensity = interp1d(intfcn(np.arange(curr_slice.shape[0])),
113-
curr_slice, axis=0, bounds_error=False, kind='linear', fill_value='extrapolate')
114+
curr_slice, axis=0, bounds_error=False, kind=interp_kind_spectral,
115+
fill_value='extrapolate')
114116

115117
y_idx = find_nearest(y_vec, curr_y_pos)[1]
116118
output_cls_instance.data[y_idx, ...] = int_fcn_intensity(x_vec)
@@ -169,7 +171,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
169171
output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
170172
fid[dset_list].read_direct(output_cls_instance.data)
171173

172-
# output_cls_instance.data = fid[dset_list].value
173174
output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
174175
elif isinstance(dset_list, list):
175176
if len(dset_list) > 1:
@@ -198,9 +199,8 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
198199
output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
199200
fid[dset_list].read_direct(output_cls_instance.data)
200201
else:
201-
output_cls_instance.data = fid[dset_list].value.astype(dset_dtype_import)
202+
output_cls_instance.data = fid[dset_list][:].astype(dset_dtype_import)
202203

203-
# output_cls_instance.data = fid[dset_list].value
204204
output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
205205

206206
elif isinstance(dset_list, list):
@@ -222,7 +222,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
222222
output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
223223
fid[dset_list].read_direct(output_cls_instance.data)
224224

225-
# output_cls_instance.data = fid[dset_list].value
226225
output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
227226
elif isinstance(dset_list, list):
228227
if len > 1:
@@ -249,7 +248,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
249248
data = np.zeros(dset_shp, dtype=dset_dtype_import)
250249
fid[dset_list].read_direct(data)
251250

252-
# data = fid[dset_list].value
253251
meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
254252
elif isinstance(dset_list, list):
255253
for num, dname in enumerate(dset_list):

‎crikit/io/macros.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,9 +15,11 @@
1515
__all__ = ['import_hdf_nist_special', 'import_csv_nist_special1']
1616

1717

18-
def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance):
18+
def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance,
19+
interp_kind_spatial='linear', interp_kind_spectral='linear'):
1920
print('\n')
20-
import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance)
21+
import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance,
22+
interp_kind_spatial='linear', interp_kind_spectral='linear')
2123
if import_success is False:
2224
raise ValueError('hdf_import_data_macroraster failed')
2325
return False

‎crikit/io/meta_process.py‎

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Original file line numberDiff line numberDiff line change
@@ -187,8 +187,16 @@ def meta_process(rosetta, output_cls_instance):
187187
stop = output_cls_instance.shape[1]-1
188188
units = 'pix'
189189

190+
if isinstance(start, _np.ndarray):
191+
start = start[0]
192+
if isinstance(stop, _np.ndarray):
193+
stop = stop[0]
194+
if isinstance(steps, _np.ndarray):
195+
steps = steps[0]
196+
190197
print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps))
191198
# print('Start: {}, Stop: {}, Steps: {}'.format(start, stop, steps))
199+
192200
output_cls_instance.x_rep.data = _np.squeeze(_np.linspace(start, stop, steps))
193201
output_cls_instance.x_rep.units = units
194202
output_cls_instance.x_rep.label = label
@@ -224,6 +232,13 @@ def meta_process(rosetta, output_cls_instance):
224232
if isinstance(label, bytes):
225233
label = label.decode()
226234

235+
if isinstance(start, _np.ndarray):
236+
start = start[0]
237+
if isinstance(stop, _np.ndarray):
238+
stop = stop[0]
239+
if isinstance(steps, _np.ndarray):
240+
steps = steps[0]
241+
227242
if steps != output_cls_instance.shape[0]:
228243
print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps))
229244
print('Warning: {}Steps assigned in meta data ({}) disagrees with datacube size ({})'.format(label, steps, output_cls_instance.shape[0]))

‎docs/build/doctrees/crikit.io.doctree‎

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Binary file not shown.

‎docs/build/html/.buildinfo‎

Lines changed: 1 addition & 1 deletion
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@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: 79acee3da732a2077d4e910c14203444
3+
config: 126e78dc37b63522d8e4d07dce0d2051
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tags: 645f666f9bcd5a90fca523b33c5a78b7

‎docs/build/html/_modules/crikit/CRIkitUI.html‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<head>
66
<meta charset="utf-8" />
77
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
8-
<title>crikit.CRIkitUI &#8212; CRIKit2 0.4.3 documentation</title>
8+
<title>crikit.CRIkitUI &#8212; CRIKit2 0.4.4 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
1010
<link rel="stylesheet" type="text/css" href="../../_static/nature.css" />
1111
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
2424
<li class="right" >
2525
<a href="../../py-modindex.html" title="Python Module Index"
2626
>modules</a> |</li>
27-
<li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
27+
<li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
2828
<li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
2929
<li class="nav-item nav-item-this"><a href="">crikit.CRIkitUI</a></li>
3030
</ul>
@@ -931,9 +931,8 @@ <h1>Source code for crikit.CRIkitUI</h1><div class="highlight"><pre>
931931
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ui</span><span class="o">.</span><span class="n">actionUndo_Backup_Enabled</span><span class="o">.</span><span class="n">isChecked</span><span class="p">():</span>
932932
<span class="k">try</span><span class="p">:</span>
933933
<span class="n">_BCPre</span><span class="o">.</span><span class="n">backup_pickle</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">hsi</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">bcpre</span><span class="o">.</span><span class="n">id_list</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
934-
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
935-
<span class="n">_traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="n">limit</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
936-
<span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
934+
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
935+
<span class="n">_traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">()</span>
937936
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error in pickle backup (Undo functionality)&#39;</span><span class="p">)</span>
938937
<span class="k">else</span><span class="p">:</span>
939938
<span class="bp">self</span><span class="o">.</span><span class="n">bcpre</span><span class="o">.</span><span class="n">backed_up</span><span class="p">()</span>
@@ -3908,7 +3907,7 @@ <h3>Navigation</h3>
39083907
<li class="right" >
39093908
<a href="../../py-modindex.html" title="Python Module Index"
39103909
>modules</a> |</li>
3911-
<li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
3910+
<li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
39123911
<li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
39133912
<li class="nav-item nav-item-this"><a href="">crikit.CRIkitUI</a></li>
39143913
</ul>

‎docs/build/html/_modules/crikit/cri/algorithms/kk.html‎

Lines changed: 3 additions & 3 deletions
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@@ -5,7 +5,7 @@
55
<head>
66
<meta charset="utf-8" />
77
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
8-
<title>crikit.cri.algorithms.kk &#8212; CRIKit2 0.4.3 documentation</title>
8+
<title>crikit.cri.algorithms.kk &#8212; CRIKit2 0.4.4 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css" />
1010
<link rel="stylesheet" type="text/css" href="../../../../_static/nature.css" />
1111
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
2424
<li class="right" >
2525
<a href="../../../../py-modindex.html" title="Python Module Index"
2626
>modules</a> |</li>
27-
<li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
27+
<li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
2828
<li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &#187;</li>
2929
<li class="nav-item nav-item-this"><a href="">crikit.cri.algorithms.kk</a></li>
3030
</ul>
@@ -274,7 +274,7 @@ <h3>Navigation</h3>
274274
<li class="right" >
275275
<a href="../../../../py-modindex.html" title="Python Module Index"
276276
>modules</a> |</li>
277-
<li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
277+
<li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
278278
<li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &#187;</li>
279279
<li class="nav-item nav-item-this"><a href="">crikit.cri.algorithms.kk</a></li>
280280
</ul>

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