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import core.modules
import core.modules.module_registry
from core.modules.vistrails_module import Module, ModuleError
import scipy
import scipy.interpolate
# Numpy package imports
import Array
import ArrayAccess
import ArrayOperations
import ArrayUtilities
import ArrayConvert
import ArrayIO
import Imaging
# Scipy package imports
import Matrix
import MatrixUtilities
import DSP
import Filters
import EnsembleOrdering
# NumSciPy plotting
import ArrayPlot
version = '0.4.0'
name = 'Num-SciPy'
identifier = 'edu.utah.sci.vistrails.numpyscipy'
def initialize(*args, **keywords):
reg = core.modules.module_registry
basic = core.modules.basic_modules
clslst = []
#########################################################################################
# Numpy Registry
reg.add_module(Array.NDArray, name="Numpy Array", namespace=Array.NDArray.my_namespace)
reg.add_output_port(Array.NDArray, "self", (Array.NDArray, 'self'))
reg.add_module(Matrix.Matrix, name="Scipy Matrix", namespace=Matrix.Matrix.my_namespace)
#########################################################################################
# Array Access registry
accessclass = [ArrayAccess.GetShape,
ArrayAccess.GetReals,
ArrayAccess.GetImaginaries,
ArrayAccess.GetMax,
ArrayAccess.GetMean,
ArrayAccess.GetMin,
ArrayAccess.GetDiagonal,
ArrayAccess.GetArrayAsType,
ArrayAccess.GetConjugate,
ArrayAccess.GetFlattenedArray,
ArrayAccess.GetField,
ArrayAccess.ToScalar,
ArrayAccess.GetMemoryFootprint,
ArrayAccess.GetArrayRank,
ArrayAccess.GetNonZeroEntries,
ArrayAccess.GetArraySize,
ArrayAccess.GetTranspose,
ArrayAccess.GetRowRange,
ArrayAccess.GetColumnRange,
ArrayAccess.GetRows]
for cls in accessclass:
cls.register(reg, basic)
#########################################################################################
# Array Operations registry
opclasses = [ArrayOperations.ArrayReshape,
ArrayOperations.ArrayCumulativeSum,
ArrayOperations.ArraySort,
ArrayOperations.ArrayCumulativeProduct,
ArrayOperations.ArrayFill,
ArrayOperations.ArrayResize,
ArrayOperations.ArrayExtractRegion,
ArrayOperations.ArrayRavel,
ArrayOperations.ArrayRound,
ArrayOperations.ArrayGetSigma,
ArrayOperations.ArraySum,
ArrayOperations.ArrayElementMultiply,
ArrayOperations.ArraySetElement,
ArrayOperations.ArrayVariance,
ArrayOperations.ArrayTrace,
ArrayOperations.ArraySwapAxes,
ArrayOperations.ArraySqueeze,
ArrayOperations.ArrayScalarMultiply,
ArrayOperations.ArrayAdd,
ArrayOperations.ArrayScalarAdd,
ArrayOperations.ArrayLog10,
ArrayOperations.ArrayAtan2,
ArrayOperations.ArraySqrt,
ArrayOperations.ArrayThreshold,
ArrayOperations.ArrayWindow,
ArrayOperations.ArrayNormalize,
ArrayOperations.ArrayName]
for cls in opclasses:
cls.register(reg, basic)
#########################################################################################
# Array Convert registry
convertclasses = [ArrayConvert.ArrayDumpToFile,
ArrayConvert.ArrayDumpToString,
ArrayConvert.ArrayToFile,
ArrayConvert.ArrayToString,
ArrayConvert.ArrayToMatrix,
ArrayConvert.ArrayToVTKImageData]
for cls in convertclasses:
cls.register(reg, basic)
#########################################################################################
# Array IO registry
ioclasses = [ArrayIO.ReadRAW,
ArrayIO.ReadNHDR,
ArrayIO.WriteRAW,
ArrayIO.WriteNHDR,
ArrayIO.ReadStatisticalSummary]
try:
import pylab
ioclasses.append(ArrayIO.ReadPNG)
ioclasses.append(ArrayIO.WritePNG)
except:
pass
for cls in ioclasses:
cls.register(reg, basic)
#########################################################################################
# Array Imaging registry
ar_util = [ArrayUtilities.ArrayToVTKScalars,
ArrayUtilities.ArrayToTimeVaryingVTKScalars,
ArrayUtilities.ArrayToTimeVaryingVTKVectors,
ArrayUtilities.ArrayToVTKVectors,
ArrayUtilities.VTKDataSetToPointArray]
clslst.extend(ar_util)
for cls in ar_util:
cls.register(reg, basic)
#########################################################################################
# Array Imaging registry
imclasses = [Imaging.ExtractRGBAChannel,
Imaging.GaussianGradientMagnitude,
Imaging.JointHistogram,
Imaging.GaussianSmooth,
Imaging.MedianFilter,
Imaging.ImageDifference,
Imaging.ImageNormalize,
Imaging.SobelGradientMagnitude]
for cls in imclasses:
cls.register(reg, basic)
#########################################################################################
# Scipy Registry
matrixclasses = [Matrix.MatrixMultiply,
Matrix.MatrixConjugate,
Matrix.MatrixToArray]
for cls in matrixclasses:
cls.register(reg,basic)
#########################################################################################
# Scipy Matrix Utilities Registry
matrixutils = [MatrixUtilities.MatlabReader,
MatrixUtilities.MatlabWriter]
for cls in matrixutils:
cls.register(reg, basic)
#########################################################################################
# Scipy DSP Registry
dspclasses = [DSP.FFT,
DSP.FFTN,
DSP.SignalSmoothing,
DSP.ShortTimeFourierTransform,
DSP.SignalGenerator]
# DSP.FrequencyPhaseLocking,
# DSP.SingleTrialPhaseLocking
try:
import smt
import Stockwell
dspclasses.append(Stockwell.StockwellTransform)
dspclasses.append(Stockwell.MultiTaperStockwellTransform)
dspclasses.append(Stockwell.FastStockwell3D)
dspclasses.append(Stockwell.Stockwell2D)
dspclasses.append(Stockwell.PyStockwellTransform)
dspclasses.append(Stockwell.PointBasedStockwell)
dspclasses.append(Stockwell.ScaleSpaceHistogram)
dspclasses.append(Stockwell.PyScaleSpaceHistogram)
dspclasses.append(Stockwell.MaximalScaleVolume)
dspclasses.append(Stockwell.ScaleVolumes)
dspclasses.append(Stockwell.IsotropicScaleVolumes)
dspclasses.append(Stockwell.FrequencyPhaseLocking)
except:
pass
for cls in dspclasses:
cls.register(reg, basic)
#########################################################################################
# Scipy Interpolation Registry
interpclasses = []
try:
import ArrayInterpolate
interpclasses.append(ArrayInterpolate.RBFInterpolate)
interpclasses.append(ArrayInterpolate.BSplineInterpolate)
except:
pass
interpclasses.append(ArrayInterpolate.BSplineResample)
for cls in interpclasses:
cls.register(reg, basic)
#########################################################################################
# Scipy Windows Registry
winclasses = [Filters.HanningWindow,
Filters.TriangularWindow,
Filters.BlackmanWindow,
Filters.BlackmanHarrisWindow,
Filters.ParzenWindow,
Filters.HammingWindow,
Filters.KaiserWindow,
Filters.BartlettHannWindow,
Filters.GaussianWindow,
Filters.BoxcarWindow,
Filters.BohmanWindow,
Filters.BartlettWindow,
Filters.NuttallBlackmanHarrisWindow]
for cls in winclasses:
cls.register(reg, basic)
#########################################################################################
# Scipy Signal Ensembles Registry
ensembles = [EnsembleOrdering.OrderByIndexes,
EnsembleOrdering.OrderByCorrelation,
EnsembleOrdering.OrderByProgressiveCorrelation,
EnsembleOrdering.ComputeDistance]
for cls in ensembles:
cls.register(reg, basic)
#########################################################################################
# NumSciPy Plotting Registry
pl = [ArrayPlot.LinePlot,
ArrayPlot.ScatterPlot,
ArrayPlot.BarChart,
ArrayPlot.Histogram,
ArrayPlot.ArrayImage]
for cls in pl:
cls.register(reg, basic)
clslst.extend(pl)
#########################################################################################
# Register all ports.
for cls in clslst:
cls.register_ports(reg, basic)
def package_dependencies():
import core.packagemanager
manager = core.packagemanager.get_package_manager()
if manager.has_package('edu.utah.sci.vistrails.vtk'):
return ['edu.utah.sci.vistrails.vtk']
else:
return []
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