1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
|
#/*##########################################################################
# Copyright (C) 2004-2014 V.A. Sole, European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
"""
This plugin offers 4 methods for rearranging spectra within the stack data
cube:
- Reverse Odd Rows
- Reverse Even Rows
- Reverse Odd Columns
- Reverse Even Columns
"""
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import numpy
import logging
from PyMca5 import StackPluginBase
_logger = logging.getLogger(__name__)
class ReverseStackPlugin(StackPluginBase.StackPluginBase):
def __init__(self, stackWindow, **kw):
if _logger.getEffectiveLevel() == logging.DEBUG:
StackPluginBase.pluginBaseLogger.setLevel(logging.DEBUG)
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
self.methodDict = {}
text = "Replace current stack by one\n"
text += "with odd rows reversed."
function = self.reverseOddRows
info = text
icon = None
self.methodDict["Reverse Odd Rows"] = [function,
info,
icon]
text = "Replace current stack by one\n"
text += "with even rows reversed."
function = self.reverseEvenRows
info = text
icon = None
self.methodDict["Reverse Even Rows"] = [function,
info,
icon]
text = "Replace current stack by one\n"
text += "with odd columns reversed."
function = self.reverseOddColumns
info = text
icon = None
self.methodDict["Reverse Odd Columns"] = [function,
info,
icon]
text = "Replace current stack by one\n"
text += "with odd columns reversed."
function = self.reverseEvenColumns
info = text
icon = None
self.methodDict["Reverse Even Columns"] = [function,
info,
icon]
self.__methodKeys = ["Reverse Odd Rows",
"Reverse Even Rows",
"Reverse Odd Columns",
"Reverse Even Columns"]
#Methods implemented by the plugin
def getMethods(self):
return self.__methodKeys
def getMethodToolTip(self, name):
return self.methodDict[name][1]
def getMethodPixmap(self, name):
return self.methodDict[name][2]
def applyMethod(self, name):
return self.methodDict[name][0]()
def reverseOddRows(self):
self.reverseRows(offset=1)
self.reversePositioners(offset=1, direction="rows")
def reverseEvenRows(self):
self.reverseRows(offset=0)
self.reversePositioners(offset=0, direction="rows")
def reverseOddColumns(self):
self.reverseColumns(offset=1)
self.reversePositioners(offset=1, direction="columns")
def reverseEvenColumns(self):
self.reverseColumns(offset=0)
self.reversePositioners(offset=0, direction="columns")
def reverseRows(self, offset=1):
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
ndata = stack.data.shape[1]
limit = 0.5 * ndata
for i in range(offset, stack.data.shape[0], 2):
j = 0
while j < limit:
tmp = stack.data[i, j, :] * 1
stack.data[i, j, :] = stack.data[i,(ndata-j-1),:] * 1
stack.data[i,(ndata-j-1),:] = tmp
j += 1
elif mcaIndex == 0:
ndata = stack.data.shape[2]
limit = 0.5 * ndata
for i in range(offset, stack.data.shape[1], 2):
j = 0
while j < limit:
tmp = stack.data[:, i, j] * 1
stack.data[:, i, j] = stack.data[:, i,(ndata-j-1)] * 1
stack.data[:, i,(ndata-j-1)] = tmp
j += 1
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
self.setStack(stack)
def reverseColumns(self, offset=1):
stack = self.getStackDataObject()
if not isinstance(stack.data, numpy.ndarray):
text = "This method does not work with dynamically loaded stacks"
raise TypeError(text)
mcaIndex = stack.info.get('McaIndex', -1)
if mcaIndex in [-1, 2]:
ndata = stack.data.shape[0]
limit = 0.5 * ndata
for i in range(offset, stack.data.shape[1], 2):
j = 0
while j < limit:
tmp = stack.data[j, i, :] * 1
stack.data[j, i, :] = stack.data[(ndata-j-1), i,:] * 1
stack.data[(ndata-j-1), i,:] = tmp
j += 1
elif mcaIndex == 0:
ndata = stack.data.shape[1]
limit = 0.5 * ndata
for i in range(offset, stack.data.shape[2], 2):
j = 0
while j < limit:
tmp = stack.data[:, j, i] * 1
stack.data[:, j, i] = stack.data[:,(ndata-j-1), i] * 1
stack.data[:, (ndata-j-1), i] = tmp
j += 1
else:
raise ValueError("Invalid 1D index %d" % mcaIndex)
self.setStack(stack)
def reversePositioners(self, offset=1, direction="rows"):
"""Re-arrange positioners data to preserve the match between
a pixel of the stack image and the corresponding values when
reversing half the rows or half the columns.
:param int offset: 1 to reverse odd rows orcolumns,
0 to reverse even ones.
:param str direction: "rows" or "columns"
"""
assert direction in ["rows", "columns"]
stackImageShape = self.getStackOriginalImage().shape
positioners = self.getStackInfo().get("positioners", None)
if positioners is None:
return
newPositioners = {}
for motorName, motorValues in positioners.items():
if numpy.isscalar(motorValues) or (hasattr(motorValues, "ndim") and
motorValues.ndim == 0):
# scalar
newPositioners[motorName] = motorValues
else:
# non-scalar positioners are always stored as arrays in info
originalShape = motorValues.shape
motorValues2d = numpy.array(motorValues, copy=True)
motorValues2d.shape = stackImageShape
if direction == "rows":
motorValues2d[offset::2] = numpy.fliplr(motorValues2d[offset::2])
elif direction == "columns":
motorValues2d[:, offset::2] = numpy.flipud(motorValues2d[:, offset::2])
newPositioners[motorName] = motorValues2d.reshape(originalShape)
self._stackWindow.setPositioners(newPositioners)
MENU_TEXT = "Stack Row or Column Reversing"
def getStackPluginInstance(stackWindow, **kw):
ob = ReverseStackPlugin(stackWindow)
return ob
|
