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
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
|
import core.modules
from core.modules.vistrails_module import Module, ModuleError
import numpy
from Array import *
class ArrayAccess(object):
my_namespace = "numpy|array|access"
class GetShape(Module, ArrayAccess):
""" Get the size of each dimension of an N-dimensional array"""
def compute(self):
a = self.getInputFromPort("Array")
sh = a.get_shape()
dims = len(sh)
for i in xrange(dims):
pname = "dim" + str(i)
self.setResult(pname, sh[i])
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Array Shape", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "dim0", (basic.Integer, 'Dim 0 Size'))
reg.add_output_port(cls, "dim1", (basic.Integer, 'Dim 1 Size'))
reg.add_output_port(cls, "dim2", (basic.Integer, 'Dim 2 Size'))
reg.add_output_port(cls, "dim3", (basic.Integer, 'Dim 3 Size'), True)
reg.add_output_port(cls, "dim4", (basic.Integer, 'Dim 4 Size'), True)
reg.add_output_port(cls, "dim5", (basic.Integer, 'Dim 5 Size'), True)
reg.add_output_port(cls, "dim6", (basic.Integer, 'Dim 6 Size'), True)
reg.add_output_port(cls, "dim7", (basic.Integer, 'Dim 7 Size'), True)
class GetReals(Module, ArrayAccess):
""" Get the real component of a complex array """
def compute(self):
a = self.getInputFromPort("Array")
b = a.get_reals()
out = NDArray()
out.set_array(b)
self.setResult("Real Component", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Reals", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Real Component", (NDArray, 'Real Components'))
class GetImaginaries(Module, ArrayAccess):
""" Get the imaginary component of a complex array """
def compute(self):
a = self.getInputFromPort("Array")
b = a.get_imaginary()
out = NDArray()
out.set_array(b)
self.setResult("Im Component", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Imaginaries", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Im Component", (NDArray, 'Imaginary Components'))
class GetMax(Module, ArrayAccess):
""" Get the maximal value from an array """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Max", float(a.get_max()))
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Max", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Max", (basic.Float, 'Max Value'))
class GetMean(Module, ArrayAccess):
""" Get the mean value of an array """
def compute(self):
a = self.getInputFromPort("Array")
axis = self.forceGetInputFromPort("Axis")
out = NDArray()
out.set_array(numpy.array(a.get_mean(axis)))
self.setResult("Mean", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Mean", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'), True)
reg.add_output_port(cls, "Mean", (NDArray, 'Mean Value'))
class GetMin(Module, ArrayAccess):
""" Get the smallest value in an array """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Min", float(a.get_min()))
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Min", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Min", (basic.Float, 'Min Value'))
class GetDiagonal(Module, ArrayAccess):
""" Get an array representing the values on the diagonal of the input array """
def compute(self):
a = self.getInputFromPort("Array")
out = NDArray()
out.set_array(a.get_diagonal())
self.setResult("Diagonal", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Diagonal", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Diagonal", (NDArray, 'Diagonal Elements'))
class GetArrayAsType(Module, ArrayAccess):
""" Cast the array to the given type """
def compute(self):
a = self.getInputFromPort("Array")
t = self.getInputFromPort("Type")
t.setValue("0")
out = NDArray()
out.set_array(a.get_array_as_type(type(t.value)))
self.setResult("Output", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Cast Array", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Type", (basic.Constant, 'Cast To Type'))
reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
class GetConjugate(Module, ArrayAccess):
""" Get the complex conjugate of the input array """
def compute(self):
a = self.getInputFromPort("Array")
out = NDArray()
out.set_array(a.get_conjugate())
self.setResult("Conjugate", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Conjugate", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Conjugate", (NDArray, 'Complex Conjugate'))
class GetFlattenedArray(Module, ArrayAccess):
""" Get a flattened representation of the input array"""
def compute(self):
a = self.getInputFromPort("Array")
out = NDArray()
out.set_array(a.get_flattened())
self.setResult("Flat Array", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Flattened Array", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Flat Array", (NDArray, 'Output Vector'))
class GetField(Module, ArrayAccess):
""" Get a field from an array given the output datatype and offset into the array"""
def compute(self):
a = self.getInputFromPort("Array")
dt = self.getInputFromPort("DType")
dt.setValue("0")
o = self.getInputFromPort("Offset")
out = NDArray()
out.set_array(a.get_field(type(dt.value), o))
self.setResult("Field", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Field", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "DType", (basic.Constant, 'Output Type'))
reg.add_input_port(cls, "Offset", (basic.Integer, 'Offset'))
reg.add_output_port(cls, "Field", (NDArray, 'Output Field'))
class ToScalar(Module, ArrayAccess):
""" Return an array of size 1 to a scalar """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Item", float(a.get_item()))
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="To Scalar", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Item", (basic.Float, 'Item'))
class GetMemoryFootprint(Module, ArrayAccess):
""" Return the amount of system memory consumed by the array """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Size", int(a.get_mem_size()))
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Memory Size", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'InputArray'))
reg.add_output_port(cls, "Size", (basic.Integer, 'Memory Size'))
class GetArrayRank(Module, ArrayAccess):
""" Get the rank of the array """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Rank", int(a.get_num_dims()))
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Array Rank", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Rank", (basic.Integer, 'Array Rank'))
class GetNonZeroEntries(Module, ArrayAccess):
""" Get an array consisting of the indices to all non-zero entries of the input array."""
def compute(self):
a = self.getInputFromPort("Array")
out = NDArray()
out.set_array(a.get_nonzero_indices())
self.setResult("Entries", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Non-Zero Entries", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Entreis", (NDArray, 'Output Array'))
class GetArraySize(Module, ArrayAccess):
""" Get the number of entries in an array """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Size", a.get_num_elements())
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Array Size", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Size", (basic.Integer, 'Number of Elements'))
class GetTranspose(Module, ArrayAccess):
""" Get the transpose of the array """
def compute(self):
a = self.getInputFromPort("Array")
out = NDArray()
out.set_array(a.get_transpose())
self.setResult("Transpose", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Get Transpose", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Transpose", (NDArray, 'Transposed Array'))
class GetRowRange(Module, ArrayAccess):
""" Get a set of rows from the input array """
def compute(self):
a = self.getInputFromPort("Array")
s = self.getInputFromPort("Start")
e = self.getInputFromPort("End")
out = NDArray()
if self.forceGetInputFromPort("One Indexed"):
s = s-1
e = e-1
out.set_array(a.get_row_range(s, e))
new_index = 0
for i in range(s,e+1):
out.set_row_name(a.get_name(i), new_index)
new_index += 1
out.set_domain_name(a.get_domain_name())
out.set_range_name(a.get_range_name())
self.setResult("Output Array", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Start", (basic.Integer, 'Start Index'))
reg.add_input_port(cls, "End", (basic.Integer, 'End Index'))
reg.add_input_port(cls, "One Indexed", (basic.Boolean, 'One Indexed'), True)
reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
class GetRows(Module, ArrayAccess):
""" Get a set of rows from the input array defined by a list of indexes """
def compute(self):
l = self.forceGetInputFromPort("Index List")
if l == None:
l = self.forceGetInputListFromPort("Indexes")
if l == None or len(l) == 0:
raise ModuleError("No indexes provided")
l.sort()
inp = self.getInputFromPort("Array")
in_ar = inp.get_array()
out_ar = in_ar[l[0],::]
for i in range(1,len(l)):
out_ar = numpy.vstack((out_ar,in_ar[i,::]))
out = NDArray()
for i in range(out_ar.shape[0]):
out.set_row_name(inp.get_row_name(l[i]), i)
out.set_array(out_ar)
out_order = NDArray()
out_order.set_array(numpy.array(l))
self.setResult("Output Array", out)
self.setResult("Output Order", out_order)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Indexes", (basic.Integer, 'Index'))
reg.add_input_port(cls, "Index List", (basic.List, 'Index List'))
reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
reg.add_output_port(cls, "Output Order", (NDArray, 'Output Ordering'))
class GetColumnRange(Module, ArrayAccess):
""" Get a set of columns from the input array """
def compute(self):
a = self.getInputFromPort("Array")
s = self.getInputFromPort("Start")
e = self.getInputFromPort("End")
out = NDArray()
out.set_array(a.get_col_range(s, e-1))
self.setResult("Output Array", out)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Start", (basic.Integer, 'Start Index'))
reg.add_input_port(cls, "End", (basic.Integer, 'End Index'))
reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
|
