Using sidpy instead of pyUSID wherever appropriate

pycroscopy/io/hdf_writer.py

@@ -15,8 +15,11 @@ from time import time, sleep
 from warnings import warn
 import h5py
 
-from pyUSID.io.hdf_utils import assign_group_index, write_simple_attrs
-from pyUSID.io.reg_ref import attempt_reg_ref_build, write_region_references
+from sidpy.hdf.hdf_utils import write_simple_attrs
+from sidpy.hdf.reg_ref import attempt_reg_ref_build, write_region_references
+
+from pyUSID.io.hdf_utils import assign_group_index
+
 from .virtual_data import VirtualGroup, VirtualDataset, VirtualData
 from ..__version__ import version
 

pycroscopy/io/translators/AR_hdf5.py

@@ -10,9 +10,10 @@ import os
 import sys
 import re  # used to get note values
 
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs, print_tree, get_attributes
 from pyUSID.io.write_utils import Dimension, make_indices_matrix
-from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, write_simple_attrs, print_tree, get_attributes
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset
 
 if sys.version_info.major == 3:
     unicode = str

pycroscopy/io/translators/be_odf.py

@@ -18,14 +18,16 @@ from scipy.io.matlab import loadmat  # To load parameters stored in Matlab .mat
 from .df_utils.be_utils import trimUDVS, getSpectroscopicParmLabel, parmsToDict, generatePlotGroups, \
     createSpecVals, requires_conjugate, generate_bipolar_triangular_waveform, \
     infer_bipolar_triangular_fraction_phase, nf32
-from pyUSID.io.reg_ref import write_region_references
-from pyUSID.io.translator import Translator
+
+from sidpy.hdf.hdf_utils import write_simple_attrs
+from sidpy.hdf.reg_ref import write_region_references
+from sidpy.sid import Translator
+from sidpy.proc.comp_utils import get_available_memory
 from pyUSID.io.write_utils import INDICES_DTYPE, VALUES_DTYPE, Dimension, calc_chunks
 from pyUSID.io.hdf_utils import write_ind_val_dsets, write_main_dataset, \
-    create_indexed_group, write_simple_attrs, write_book_keeping_attrs, copy_attributes,\
+    create_indexed_group, write_book_keeping_attrs, copy_attributes,\
     write_reduced_anc_dsets, get_unit_values
 from pyUSID.io.usi_data import USIDataset
-from pyUSID.processing.comp_utils import get_available_memory
 
 if sys.version_info.major == 3:
     unicode = str

pycroscopy/io/translators/be_odf_relaxation.py

@@ -9,16 +9,16 @@ from __future__ import division, print_function, absolute_import, unicode_litera
 
 from os import path, 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
 import h5py
-
-from .df_utils.be_utils import trimUDVS, getSpectroscopicParmLabel, generatePlotGroups, createSpecVals, maxReadPixels, \
-    nf32
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
 from pyUSID.io.write_utils import INDICES_DTYPE, Dimension
-from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, write_simple_attrs
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset
+
+from .df_utils.be_utils import trimUDVS, getSpectroscopicParmLabel, \
+    generatePlotGroups, createSpecVals, maxReadPixels, nf32
 
 
 class BEodfRelaxationTranslator(Translator):

pycroscopy/io/translators/beps_data_generator.py

@@ -7,11 +7,12 @@ import numpy as np
 from sklearn.utils import gen_batches
 from skimage.measure import block_reduce
 # Pycroscopy imports
-from pyUSID.io.hdf_utils import get_h5_obj_refs, link_as_main, get_attr, copy_dataset, \
-    write_main_dataset, write_simple_attrs, create_indexed_group, create_results_group, write_reduced_anc_dsets
-from pyUSID.io.dtype_utils import stack_real_to_compound
-from pyUSID.io.translator import Translator
-from pyUSID import USIDataset
+from sidpy.hdf.hdf_utils import get_attr, write_simple_attrs
+from sidpy.hdf.dtype_utils import stack_real_to_compound
+from sidpy.sid import Translator
+from pyUSID.io.hdf_utils import link_as_main, copy_dataset, \
+    write_main_dataset, create_indexed_group, create_results_group, \
+    write_reduced_anc_dsets
 from pyUSID.io.write_utils import Dimension, calc_chunks
 from pyUSID.io.image import read_image
 from ...analysis.utils.be_loop import loop_fit_function

pycroscopy/io/translators/beps_ndf.py

@@ -16,12 +16,15 @@ import numpy as np
 import xlrd as xlreader  # To read the UDVS spreadsheet
 from scipy.io.matlab import loadmat  # To load parameters stored in Matlab .mat file
 
-from .df_utils.be_utils import trimUDVS, getSpectroscopicParmLabel, parmsToDict, generatePlotGroups, \
-    normalizeBEresponse, createSpecVals, nf32
-from pyUSID.io.translator import Translator
-from pyUSID.io.write_utils import make_indices_matrix, VALUES_DTYPE, INDICES_DTYPE, calc_chunks
-from pyUSID.io.hdf_utils import get_h5_obj_refs, link_h5_objects_as_attrs
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import get_h5_obj_refs, link_h5_objects_as_attrs
+
+from pyUSID.io.write_utils import make_indices_matrix, VALUES_DTYPE, \
+    INDICES_DTYPE, calc_chunks
 from pyUSID.io.usi_data import USIDataset
+
+from .df_utils.be_utils import trimUDVS, getSpectroscopicParmLabel, \
+    parmsToDict, generatePlotGroups, normalizeBEresponse, createSpecVals, nf32
 from ..hdf_writer import HDFwriter
 from ..virtual_data import VirtualGroup, VirtualDataset
 

pycroscopy/io/translators/bruker_afm.py

@@ -11,9 +11,12 @@ from collections import OrderedDict
 import numpy as np
 import h5py
 
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import Dimension
-from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, write_simple_attrs, write_ind_val_dsets
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, \
+    write_ind_val_dsets
 from .df_utils.base_utils import read_binary_data
 # TODO: Adopt missing aspects / features from https://github.com/paruch-group/distortcorrect/blob/master/afm/filereader/readNanoscope.py
 

pycroscopy/io/translators/df_utils/be_utils.py

@@ -15,12 +15,13 @@ import matplotlib.pyplot as plt
 import numpy as np
 import xlrd as xlreader
 
-from pyUSID.io.hdf_utils import get_auxiliary_datasets, find_dataset, \
-    link_h5_objects_as_attrs, get_attr, create_indexed_group, \
-    write_simple_attrs, write_main_dataset, get_unit_values
+from sidpy.hdf.hdf_utils import write_simple_attrs, link_h5_objects_as_attrs, \
+    get_attr, get_auxiliary_datasets
+from sidpy.proc.comp_utils import get_available_memory, parallel_compute
 
+from pyUSID.io.hdf_utils import find_dataset, create_indexed_group, \
+    write_main_dataset, get_unit_values
 from pyUSID.io.write_utils import create_spec_inds_from_vals, Dimension
-from pyUSID.processing.comp_utils import get_available_memory, parallel_compute
 
 from ....processing.histogram import build_histogram
 from ....analysis.utils.be_sho import SHOestimateGuess

pycroscopy/io/translators/forc_iv.py

@@ -12,9 +12,11 @@ import h5py
 import numpy as np  # For array operations
 from scipy.io import loadmat
 
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import Dimension
-from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group, write_simple_attrs
+from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group
 
 
 class ForcIVTranslator(Translator):

pycroscopy/io/translators/general_dynamic_mode.py

@@ -13,11 +13,13 @@ import numpy as np  # For array operations
 from scipy.io.matlab import loadmat  # To load parameters stored in Matlab .mat file
 import h5py
 
-from .df_utils.gmode_utils import readGmodeParms
-from pyUSID.io.translator import Translator  # Because this class extends the abstract Translator class
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs, link_h5_objects_as_attrs
+
 from pyUSID.io.write_utils import VALUES_DTYPE, Dimension
-from pyUSID.io.hdf_utils import link_h5_objects_as_attrs, create_indexed_group, \
-    write_simple_attrs, write_main_dataset
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset
+
+from .df_utils.gmode_utils import readGmodeParms
 
 
 class GDMTranslator(Translator):

pycroscopy/io/translators/general_mode_vs.py

@@ -13,11 +13,13 @@ import numpy as np  # For array operations
 from scipy.io.matlab import loadmat  # To load parameters stored in Matlab .mat file
 import h5py
 
-from .df_utils.gmode_utils import readGmodeParms
-from pyUSID.io.translator import Translator  # Because this class extends the abstract Translator class
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs, link_h5_objects_as_attrs
+
 from pyUSID.io.write_utils import VALUES_DTYPE, Dimension
-from pyUSID.io.hdf_utils import link_h5_objects_as_attrs, create_indexed_group, \
-    write_simple_attrs, write_main_dataset
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset
+
+from .df_utils.gmode_utils import readGmodeParms
 
 
 class GVSTranslator(Translator):
@@ -59,7 +61,7 @@ class GVSTranslator(Translator):
         #parm_dict['freq_sweep_delay'] = np.float(freq_sweep_parms['delay'].item())
         gen_sig = parm_data['genSig']
         #parm_dict['wfm_fix_d_fast'] = np.int32(gen_sig['restrictT'].item())
-        #freq_array = np.float32(parm_data['freqArray'])
+        freq_array = np.float32(parm_data['freqArray'])
 
         # prepare and write spectroscopic values
         samp_rate = parm_dict['IO_down_samp_rate_[Hz]']

pycroscopy/io/translators/gmode_iv.py

@@ -13,9 +13,11 @@ from warnings import warn
 import h5py
 import numpy as np  # For array operations
 
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import Dimension
-from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group, write_simple_attrs
+from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group
 
 
 class GIVTranslator(Translator):

pycroscopy/io/translators/gmode_line.py

@@ -12,10 +12,14 @@ import h5py
 import numpy as np
 from scipy.io.matlab import loadmat  # To load parameters stored in Matlab .mat file
 
-from .df_utils.be_utils import parmsToDict
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import VALUES_DTYPE, Dimension
-from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group, write_simple_attrs, write_ind_val_dsets
+from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group, \
+    write_ind_val_dsets
+
+from .df_utils.be_utils import parmsToDict
 
 if sys.version_info.major == 3:
     unicode = str

pycroscopy/io/translators/gmode_tune.py

@@ -14,10 +14,14 @@ import h5py
 import numpy as np
 from scipy.io.matlab import loadmat  # To load parameters stored in Matlab .mat file
 
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
+from pyUSID.io.write_utils import VALUES_DTYPE, Dimension
+from pyUSID.io.hdf_utils import create_indexed_group, write_ind_val_dsets, \
+    write_main_dataset
+
 from .df_utils.be_utils import parmsToDict
 from .gmode_line import GLineTranslator
-from pyUSID.io.write_utils import VALUES_DTYPE, Dimension
-from pyUSID.io.hdf_utils import write_simple_attrs, create_indexed_group, write_ind_val_dsets, write_main_dataset
 
 
 class GTuneTranslator(GLineTranslator):

pycroscopy/io/translators/gwyddion.py

@@ -11,9 +11,12 @@ import sys
 import numpy as np
 import h5py
 
-from pyUSID.io.translator import Translator
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import Dimension
-from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, write_simple_attrs, write_ind_val_dsets
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, \
+    write_ind_val_dsets
 
 # packages specific to this kind of file
 from .df_utils.gsf_read import gsf_read

pycroscopy/io/translators/igor_ibw.py

@@ -12,9 +12,12 @@ import numpy as np  # For array operations
 import h5py
 from igor import binarywave as bw
 
-from pyUSID.io.translator import Translator # Because this class extends the abstract Translator class
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import VALUES_DTYPE, Dimension
-from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, write_simple_attrs, write_ind_val_dsets
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset, \
+    write_ind_val_dsets
 
 if sys.version_info.major == 3:
     unicode = str

pycroscopy/io/translators/image_stack.py

@@ -14,13 +14,16 @@ from PIL import Image
 from skimage.measure import block_reduce
 import h5py
 
-from .df_utils.image_utils import no_bin
-from .df_utils.dm_utils import read_dm3
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs, get_h5_obj_refs
+
 from pyUSID.io.image import read_image
-from pyUSID.io.translator import Translator
 from pyUSID.io.write_utils import Dimension, calc_chunks
-from pyUSID.io.hdf_utils import get_h5_obj_refs, link_as_main, write_main_dataset, \
-    write_simple_attrs, create_indexed_group
+from pyUSID.io.hdf_utils import link_as_main, write_main_dataset, \
+    create_indexed_group
+
+from .df_utils.image_utils import no_bin
+from .df_utils.dm_utils import read_dm3
 
 
 class ImageStackTranslator(Translator):

pycroscopy/io/translators/labview_h5_patcher.py

@@ -13,12 +13,15 @@ import h5py
 import os
 import numpy as np
 
-from .df_utils.be_utils import remove_non_exist_spec_dim_labs
-from pyUSID.io.translator import Translator
-from pyUSID.io.hdf_utils import get_attr, link_as_main, find_results_groups, \
-    check_and_link_ancillary, find_dataset, write_simple_attrs
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import get_attr, write_simple_attrs
+
+from pyUSID.io.hdf_utils import link_as_main, find_results_groups, \
+    check_and_link_ancillary, find_dataset
 from pyUSID.io.write_utils import create_spec_inds_from_vals
 
+from .df_utils.be_utils import remove_non_exist_spec_dim_labs
+
 if sys.version_info.major == 3:
     unicode = str
 

pycroscopy/io/translators/nanonis.py

@@ -7,10 +7,14 @@ import os
 from warnings import warn
 import numpy as np
 import h5py
-from pyUSID.io.hdf_utils import (create_indexed_group, write_main_dataset,
-                                 write_simple_attrs, Dimension,
-                                 write_ind_val_dsets)
-from pyUSID.io.translator import Translator
+
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
+from pyUSID.io.hdf_utils import create_indexed_group, write_main_dataset,\
+    write_ind_val_dsets
+from pyUSID.io.write_utils import Dimension
+
 from .df_utils.nanonis_utils import read_nanonis_file
 # TODO: Adopt any missing features from https://github.com/paruch-group/distortcorrect/blob/master/afm/filereader/nanonisFileReader.py
 

pycroscopy/io/translators/ndata.py

@@ -16,11 +16,14 @@ import numpy as np
 from skimage.measure import block_reduce
 from skimage.util import crop
 
+from sidpy.sid import Translator
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
+from pyUSID.io.write_utils import Dimension, calc_chunks
+from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group
+
 from .df_utils.image_utils import unnest_parm_dicts
 from .df_utils.dm_utils import read_dm3
-from pyUSID.io.translator import Translator
-from pyUSID.io.write_utils import Dimension, calc_chunks
-from pyUSID.io.hdf_utils import write_main_dataset, create_indexed_group, write_simple_attrs
 
 
 class NDataTranslator(Translator):