-
Notifications
You must be signed in to change notification settings - Fork 34
Expand file tree
/
Copy pathImportNumPyArray.py
More file actions
248 lines (192 loc) · 10.1 KB
/
Copy pathImportNumPyArray.py
File metadata and controls
248 lines (192 loc) · 10.1 KB
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
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
import os
import textwrap
import vtk
import slicer
from slicer.ScriptedLoadableModule import *
class ImportNumPyArray(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
parent.title = "ImportNumPyArray"
parent.categories = ["Informatics"]
parent.dependencies = []
parent.contributors = ["Dzenan Zukic (Kitware)", "Andras Lasso (Perk Lab, Queen's University)"]
parent.helpText = textwrap.dedent("""
Reader for numpy array files (.npy and .npz).
vtkMRMLScalarVolumeNode (for 1D-3D numpy array), vtkMRMLVectorVolumeNode (for 4D), or vtkMRMLSequenceNode (for 5D)
is added to the scene. See https://numpy.org/devdocs/reference/generated/numpy.lib.format.html#npy-format
Axis order for array dimension:
- 1D: I
- 2D: J, I
- 3D: K, J, I
- 4D: K, J, I, component
- 5D: time, K, J, I, component
""")
parent.acknowledgementText = textwrap.dedent("""
This module is adapted from work done by Steve Pieper to support loading of NIfTI files.
""")
self.parent = parent
class ImportNumPyArrayWidget(ScriptedLoadableModuleWidget):
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Default reload&test widgets are enough.
# Note that reader is not reloaded.
class ImportNumPyArrayFileReader:
def __init__(self, parent):
self.parent = parent
def description(self):
return "NumPy Array Image"
def fileType(self):
return "NumPyArrayImageFile"
def extensions(self):
return ["NumPy Array Image (*.npy)", "NumPy Array Image (*.npz)"]
def canLoadFile(self, filePath):
ext = filePath[-4:].lower()
return ext == ".npy" or ext == ".npz"
def _addSequenceBrowserNode(self, baseName, outputSequenceNode, playbackRateFps):
# Add a browser node and show the volume in the slice viewer for user convenience
outputSequenceBrowserNode = slicer.vtkMRMLSequenceBrowserNode()
outputSequenceBrowserNode.SetName(slicer.mrmlScene.GenerateUniqueName(baseName + " browser"))
outputSequenceBrowserNode.SetPlaybackRateFps(playbackRateFps)
slicer.mrmlScene.AddNode(outputSequenceBrowserNode)
outputSequenceBrowserNode.AddSynchronizedSequenceNode(outputSequenceNode)
proxyVolumeNode = outputSequenceBrowserNode.GetProxyNode(outputSequenceNode)
# Show sequence browser toolbar
slicer.modules.sequences.setToolBarActiveBrowserNode(outputSequenceBrowserNode)
slicer.modules.sequences.showSequenceBrowser(outputSequenceBrowserNode)
return outputSequenceBrowserNode
def load(self, properties):
"""
uses properties:
fileName - path to the .npy or .npz file
"""
try:
import numpy as np
filePath = properties["fileName"]
# Get node base name from filename
if "name" in properties.keys():
baseName = properties["name"]
else:
baseName = os.path.splitext(os.path.basename(filePath))[0]
numpyArray = np.load(filePath)
# npz files may store multiple arrays, use only the first one
if hasattr(numpyArray, "files"):
# npz file, get the first array
if len(numpyArray.files) != 1:
raise RuntimeError(f"Input npz file must contain exactly one array, found {len(numpyArray.files)}.")
numpyArray = numpyArray[numpyArray.files[0]]
shape = numpyArray.shape
if len(shape) > 5:
raise RuntimeError("Arrays larger than 5 dimensions are not supported")
if len(shape) < 1:
raise RuntimeError("Zero dimensional arrays are not supported")
volumeClassName = 'vtkMRMLScalarVolumeNode'
if len(shape) >= 4 and shape[-1] > 1:
volumeClassName = 'vtkMRMLVectorVolumeNode'
if len(shape) < 5:
volumeNode = slicer.mrmlScene.AddNewNodeByClass(volumeClassName, slicer.mrmlScene.GenerateUniqueName(baseName))
slicer.util.updateVolumeFromArray(volumeNode, numpyArray)
volumeNode.CreateDefaultDisplayNodes()
else: # 5 dimensions
# Copy volumes into a sequence
volumeSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode", slicer.mrmlScene.GenerateUniqueName(baseName + "sequence"))
volumeNodeTemp = slicer.mrmlScene.AddNewNodeByClass(volumeClassName, "__temp__ImportNumPyArray")
for volumeIndex in range(shape[0]):
if numpyArray.shape[-1] == 1:
# Single component
slicer.util.updateVolumeFromArray(volumeNodeTemp, numpyArray[volumeIndex, :, :, :, 0])
else:
# Multiple components
slicer.util.updateVolumeFromArray(volumeNodeTemp, numpyArray[volumeIndex, :, :, :, :])
volumeSequenceNode.SetDataNodeAtValue(volumeNodeTemp, str(volumeIndex))
slicer.mrmlScene.RemoveNode(volumeNodeTemp)
# Create sequence browser node so that the image sequence can be browsed
volumeSequenceBrowserNode = self._addSequenceBrowserNode(baseName, volumeSequenceNode, 5.0)
# Use the proxy node of the sequence as output, remove the temporary volume node
volumeNode = volumeSequenceBrowserNode.GetProxyNode(volumeSequenceBrowserNode.GetMasterSequenceNode())
# Show the volume
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(volumeNode.GetID())
appLogic.PropagateVolumeSelection()
appLogic.FitSliceToAll()
except Exception as e:
import traceback
traceback.print_exc()
errorMessage = f"Failed to load numpy array file: {str(e)}"
self.parent.userMessages().AddMessage(vtk.vtkCommand.ErrorEvent, errorMessage)
return False
self.parent.loadedNodes = [volumeNode.GetID()]
return True
class ImportNumPyArrayTest(ScriptedLoadableModuleTest):
def runTest(self):
"""Run as few or as many tests as needed here."""
self.setUp()
self.testWriterReader()
self.tearDown()
self.delayDisplay("Testing complete")
def setUp(self):
self.tempDir = slicer.util.tempDirectory()
slicer.mrmlScene.Clear()
def tearDown(self):
import shutil
shutil.rmtree(self.tempDir, True)
def _testWriteReadOne(self, filename, dimension, voxelArray):
import numpy as np
shape = voxelArray.shape
assert len(shape) == dimension
npArrayPath = os.path.join(self.tempDir, f"TestImportNumPyArray_{filename}")
if filename.endswith(".npy"):
np.save(npArrayPath, voxelArray)
else:
np.savez(npArrayPath, voxelArray)
loadedVolumeNode = slicer.util.loadNodeFromFile(npArrayPath, "NumPyArrayImageFile")
if len(shape) < 5:
loadedVoxelArray = slicer.util.arrayFromVolume(loadedVolumeNode)
self.assertTrue(np.allclose(voxelArray, loadedVoxelArray))
else:
browserNode = slicer.modules.sequences.logic().GetFirstBrowserNodeForProxyNode(loadedVolumeNode)
for sequenceItemIndex in [0, 3, 7]:
browserNode.SetSelectedItemNumber(sequenceItemIndex)
loadedVoxelArray = slicer.util.arrayFromVolume(loadedVolumeNode)
self.assertTrue(np.allclose(voxelArray[sequenceItemIndex, :, :, :, 0], loadedVoxelArray))
def testWriterReader0D(self):
import numpy as np
with self.assertRaisesRegex(RuntimeError, "Zero dimensional arrays are not supported"):
self._testWriteReadOne("0d.npy", 0, np.array(0))
def testWriterReader6D(self):
import numpy as np
with self.assertRaisesRegex(RuntimeError, "Arrays larger than 5 dimensions are not supported"):
self._testWriteReadOne("6d.npy", 6, np.zeros([3, 5, 2, 5, 2, 6]))
def testWriterReader1D2D3D(self):
import numpy as np
import SampleData
inputVolume = SampleData.SampleDataLogic().downloadMRHead()
input3dArray = slicer.util.arrayFromVolume(inputVolume)
self._testWriteReadOne("3d.npy", 3, input3dArray)
self._testWriteReadOne("3d.npz", 3, input3dArray)
self._testWriteReadOne("2d.npy", 2, input3dArray[20, :])
self._testWriteReadOne("1d.npy", 1, input3dArray[30, 20, :])
def testWriterReader4D(self):
import numpy as np
import SampleData
inputVolume = SampleData.SampleDataLogic().downloadMRHead()
input3dArray = slicer.util.arrayFromVolume(inputVolume)
input4dArray = np.zeros([input3dArray.shape[0], input3dArray.shape[1], input3dArray.shape[2], 3])
input4dArray[:, :, :, 0] = input3dArray
input4dArray[:, :, :, 1] = input3dArray + 50
input4dArray[:, :, :, 2] = input3dArray - 30
self._testWriteReadOne("4d.npy", 4, input4dArray)
def testWriterReader5D(self):
import numpy as np
import SampleData
sequenceNode = SampleData.downloadSample('CTCardioSeq')
sequenceBrowserNode = slicer.modules.sequences.logic().GetFirstBrowserNodeForSequenceNode(sequenceNode)
sequenceNode = sequenceBrowserNode.GetMasterSequenceNode()
# Preallocate a 5D numpy array that will hold the entire sequence
import numpy as np
dims = slicer.util.arrayFromVolume(sequenceNode.GetNthDataNode(0)).shape
voxelArray = np.zeros([sequenceNode.GetNumberOfDataNodes(), dims[0], dims[1], dims[2], 1])
# Fill in the 4D array from the sequence node
for volumeIndex in range(sequenceNode.GetNumberOfDataNodes()):
voxelArray[volumeIndex, :, :, :, 0] = slicer.util.arrayFromVolume(sequenceNode.GetNthDataNode(volumeIndex))
self._testWriteReadOne("5d.npy", 5, voxelArray)