Porting of Image Transformation and Feature Extraction routines.

pycroscopy/analysis/utils/be_loop.py

@@ -8,13 +8,15 @@ Various helper functions for aiding loop fitting and projection
 """
 
 from __future__ import division
-from scipy.special import erf, erfinv
+
+import matplotlib.pyplot as plt
 import numpy as np
 from scipy import stats
 from scipy.optimize import least_squares
-from scipy.spatial import ConvexHull
-import matplotlib.pyplot as plt
 from scipy.optimize import leastsq
+from scipy.spatial import ConvexHull
+from scipy.special import erf, erfinv
+
 
 ###############################################################################
 

pycroscopy/io/microdata.py

@@ -5,10 +5,12 @@ Created on Wed Dec 16 10:42:03 2015
 @author: Suhas Somnath, Numan Laanait
 
 """
-from warnings import warn
 import socket
+from warnings import warn
+
 from .io_utils import getTimeStamp
 
+
 class MicroData(object):
     '''
     Generic class that is extended by the MicroDataGroup and MicroDataset objects

pycroscopy/io/translators/be_odf.py

@@ -6,18 +6,22 @@ Created on Tue Nov  3 15:24:12 2015
 """
 
 from __future__ import division; # int/int = float
-import numpy as np; # For array operations
-from warnings import warn
+
 from os import path, listdir, remove # File Path formatting
+from warnings import warn
+
+import numpy as np; # For array operations
 from scipy.io.matlab import loadmat; # To load parameters stored in Matlab .mat file
+
+from .be_utils import trimUDVS, getSpectroscopicParmLabel, parmsToDict, generatePlotGroups, createSpecVals
 from .translator import Translator # Because this class extends the abstract Translator class
 from .utils import makePositionMat, getPositionSlicing, generateDummyMainParms
-from .be_utils import trimUDVS, getSpectroscopicParmLabel, parmsToDict, generatePlotGroups, createSpecVals
-from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
-from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
-from ..hdf_utils import getH5DsetRefs, linkRefs
 from ..be_hdf_utils import maxReadPixels
-     
+from ..hdf_utils import getH5DsetRefs, linkRefs
+from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
+from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
+
+
 class BEodfTranslator(Translator):
     """
     Translates either the Band Excitation (BE) scan or Band Excitation 

pycroscopy/io/translators/be_utils.py

@@ -8,18 +8,18 @@ Created on Tue Jan 05 07:55:56 2016
 from os import path
 from warnings import warn
 
+import h5py
 import matplotlib.pyplot as plt
 import numpy as np
 
-from ..hdf_utils import getH5DsetRefs
-from ..microdata import MicroDataset,MicroDataGroup
 from ..be_hdf_utils import getActiveUDVSsteps,maxReadPixels
-from ..io_utils import getAvailableMem
 from ..hdf_utils import getAuxData, getDataSet, getH5DsetRefs, linkRefs
 from ..io_hdf5 import ioHDF5
-from ...viz.plot_utils import plot1DSpectrum, plot2DSpectrogram, plotHistgrams
+from ..io_utils import getAvailableMem
+from ..microdata import MicroDataset,MicroDataGroup
 from ...processing.proc_utils import buildHistogram
-import h5py
+from ...viz.plot_utils import plot1DSpectrum, plot2DSpectrogram, plotHistgrams
+
 
 #%%############################################################################
 

pycroscopy/io/translators/fast_iv.py

@@ -6,15 +6,19 @@ Created on Sun May 29 17:58:35 2016
 """
 
 from __future__ import division # int/int = float
-import numpy as np # For array operations
+
 from os import path, remove # File Path formatting
 from warnings import warn
+
 import h5py
+import numpy as np # For array operations
+
 from .translator import Translator
 from .utils import makePositionMat, getPositionSlicing, generateDummyMainParms
-from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
-from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
 from ..hdf_utils import getH5DsetRefs, linkRefs
+from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
+from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
+
 
 class FastIVTranslator(Translator):
     """

pycroscopy/io/translators/general_dynamic_mode.py

@@ -6,15 +6,19 @@ Created on Fri Mar 04 11:12:45 2016
 """
 
 from __future__ import print_function, division # int/int = float
-import numpy as np # For array operations
+
 from os import path, remove# File Path formatting
+
+import numpy as np # For array operations
 from scipy.io.matlab import loadmat # To load parameters stored in Matlab .mat file
+
+from .gmode_utils import readGmodeParms
 from .translator import Translator # Because this class extends the abstract Translator class
 from .utils import makePositionMat, getPositionSlicing, generateDummyMainParms
-from .gmode_utils import readGmodeParms
-from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
-from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
 from ..hdf_utils import getH5DsetRefs, linkRefs
+from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
+from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
+
 
 class GDMTranslator(Translator):
     """

pycroscopy/io/translators/gmode_line.py

@@ -5,16 +5,20 @@ Created on Sat Nov 07 15:21:46 2015
 @author: Suhas Somnath
 """
 from __future__ import division, print_function # int/int = float
-import numpy as np # For array operations
+
 from os import path, listdir, remove # File Path formatting
 from warnings import warn
+
+import numpy as np # For array operations
 from scipy.io.matlab import loadmat # To load parameters stored in Matlab .mat file
+
+from .be_utils import parmsToDict
 from .translator import Translator
 from .utils import interpretFreq, makePositionMat, getPositionSlicing, generateDummyMainParms
-from .be_utils import parmsToDict
-from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
-from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
 from ..hdf_utils import getH5DsetRefs, linkRefs
+from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
+from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
+
 
 class GLineTranslator(Translator):
     """

pycroscopy/io/translators/ptychography.py

@@ -4,14 +4,17 @@ Created on Feb 9, 2016
 @author: Chris Smith
 """
 
-import numpy as np
 import os
+
+import numpy as np
 from scipy.misc import imread
-from ..io_hdf5 import ioHDF5
-from ..microdata import MicroDataGroup, MicroDataset
-from ..hdf_utils import getH5DsetRefs, linkRefs
+
 from .translator import Translator
 from .utils import generateDummyMainParms, makePositionMat, getPositionSlicing
+from ..hdf_utils import getH5DsetRefs, linkRefs
+from ..io_hdf5 import ioHDF5
+from ..microdata import MicroDataGroup, MicroDataset
+
 
 class PtychographyTranslator(Translator):
     """

pycroscopy/io/translators/sporc.py

@@ -6,15 +6,19 @@ Created on Tue Mar 29 16:04:34 2016
 """
 
 from __future__ import print_function, division; # int/int = float
-import numpy as np; # For array operations
+
 from os import path, remove # File Path formatting
-from scipy.io.matlab import loadmat # To load parameters stored in Matlab .mat file
+
 import h5py
+import numpy as np; # For array operations
+from scipy.io.matlab import loadmat # To load parameters stored in Matlab .mat file
+
 from .translator import Translator # Because this class extends the abstract Translator class
 from .utils import makePositionMat, getPositionSlicing, generateDummyMainParms
 from ..hdf_utils import getH5DsetRefs, linkRefs
-from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
 from ..io_hdf5 import ioHDF5 # Now the translator is responsible for writing the data.
+from ..microdata import MicroDataGroup, MicroDataset # The building blocks for defining heirarchical storage in the H5 file
+
 
 class SporcTranslator(Translator):
     """

pycroscopy/processing/cluster.py

@@ -6,11 +6,13 @@ Created on Tue Jan 05 07:55:56 2016
 """
 import numpy as np
 import sklearn.cluster as cls
-from ..io.io_hdf5 import ioHDF5
+
 from ..io.hdf_utils import checkIfMain
+from ..io.hdf_utils import getH5DsetRefs, checkAndLinkAncillary
+from ..io.io_hdf5 import ioHDF5
 from ..io.io_utils import check_dtype, transformToTargetType
 from ..io.microdata import MicroDataGroup, MicroDataset
-from ..io.hdf_utils import getH5DsetRefs, checkAndLinkAncillary
+
 
 class Cluster(object):
     """

pycroscopy/processing/decomposition.py

@@ -4,14 +4,16 @@ Created on Tue Jan 05 07:55:56 2016
 
 @author: Suhas Somnath, Chris Smith
 """
+import h5py
 import numpy as np
 import sklearn.decomposition as dec
-import h5py
-from ..io.io_hdf5 import ioHDF5
+
 from ..io.hdf_utils import checkIfMain
+from ..io.hdf_utils import getH5DsetRefs, checkAndLinkAncillary
+from ..io.io_hdf5 import ioHDF5
 from ..io.io_utils import check_dtype, transformToTargetType
 from ..io.microdata import MicroDataGroup, MicroDataset
-from ..io.hdf_utils import getH5DsetRefs, checkAndLinkAncillary
+
 
 class Decomposition(object):
     """

pycroscopy/processing/gmode_utils.py

@@ -5,16 +5,18 @@ Created on Thu May 05 13:29:12 2016
 @author: Suhas Somnath
 """
 
-import numpy as np
-import matplotlib.pyplot as plt
-from warnings import warn
-from multiprocessing import Pool, cpu_count
 import itertools
-from ..io.io_utils import getTimeStamp
-from ..io.hdf_utils import getH5DsetRefs, getH5GroupRef, linkRefs
-from ..viz.plot_utils import rainbowPlot
+from multiprocessing import Pool, cpu_count
+from warnings import warn
+
+import matplotlib.pyplot as plt
+import numpy as np
+
 from .fft import getNoiseFloor, noiseBandFilter, makeLPF, harmonicsPassFilter
+from ..io.hdf_utils import getH5DsetRefs, getH5GroupRef, linkRefs
+from ..io.io_utils import getTimeStamp
 from ..io.microdata import MicroDataGroup, MicroDataset
+from ..viz.plot_utils import rainbowPlot
 
 
 ###############################################################################

pycroscopy/processing/svd_utils.py

@@ -6,12 +6,14 @@ Created on Mon Mar 28 09:45:08 2016
 """
 
 import time
-import numpy as np
 from warnings import warn
+
+import numpy as np
 from sklearn.utils.extmath import randomized_svd
-from ..io.io_hdf5 import ioHDF5
+
 from ..io.hdf_utils import getH5DsetRefs, checkAndLinkAncillary, \
     getH5RegRefIndices, createRefFromIndices, checkIfMain
+from ..io.io_hdf5 import ioHDF5
 from ..io.io_utils import check_dtype
 from ..io.microdata import MicroDataset, MicroDataGroup
 

pycroscopy/viz/plot_utils.py

@@ -5,13 +5,16 @@ Created on Thu May 05 13:29:12 2016
 @author: Suhas Somnath
 """
 from __future__ import division # int/int = float
-import numpy as np
-import matplotlib.pyplot as plt
+
+from warnings import warn
+
 import h5py
+import matplotlib.pyplot as plt
+import numpy as np
+from mpl_toolkits.axes_grid1 import make_axes_locatable
 from scipy.cluster.hierarchy import linkage, dendrogram
 from scipy.spatial.distance import pdist
-from warnings import warn
-from mpl_toolkits.axes_grid1 import make_axes_locatable
+
 from ..analysis.utils.be_loop import loopFitFunction
 
 

setup.py

@@ -9,7 +9,7 @@ with open(path.join(here, 'README.rst')) as f:
 
 setup(
     name='pycroscopy',
-    version='0.0a3',
+    version='0.0a4',
     description='A suite of Python libraries for high performance scientific computing of microscopy data.',
     long_description= long_description,
     classifiers=[