Importing from sidpy instead of pyUSID wherever appropriate

pycroscopy/analysis/be_loop_fitter.py

@@ -20,12 +20,13 @@ from sklearn.cluster import KMeans
 from scipy.optimize import least_squares
 from scipy.cluster.hierarchy import linkage
 from scipy.spatial.distance import pdist
-from pyUSID.io.dtype_utils import stack_real_to_compound, \
+from sidpy.hdf.dtype_utils import stack_real_to_compound, \
     flatten_compound_to_real
+from sidpy.hdf.hdf_utils import get_attr, write_simple_attrs
+from sidpy.proc.comp_utils import get_MPI, recommend_cpu_cores
 from pyUSID.io.hdf_utils import get_unit_values, get_sort_order, \
-    reshape_to_n_dims, get_attr, create_empty_dataset, create_results_group, \
-    write_reduced_anc_dsets, write_simple_attrs, write_main_dataset
-from pyUSID.processing.comp_utils import get_MPI, recommend_cpu_cores
+    reshape_to_n_dims, create_empty_dataset, create_results_group, \
+    write_reduced_anc_dsets, write_main_dataset
 from pyUSID.io.usi_data import USIDataset
 from .utils.be_loop import projectLoop, fit_loop, generate_guess, \
     loop_fit_function, calc_switching_coef_vec, switching32

pycroscopy/analysis/be_sho_fitter.py

@@ -13,9 +13,9 @@ from enum import Enum
 from warnings import warn
 import numpy as np
 from functools import partial
-from pyUSID.io.hdf_utils import write_simple_attrs, \
-    create_results_group, write_reduced_anc_dsets, create_empty_dataset, \
-    write_main_dataset, get_attr
+from sidpy.hdf.hdf_utils import write_simple_attrs, get_attr
+from pyUSID.io.hdf_utils import create_results_group, write_main_dataset, \
+    write_reduced_anc_dsets, create_empty_dataset
 from pyUSID.io.usi_data import USIDataset
 
 from scipy.signal import find_peaks_cwt

pycroscopy/analysis/fitter.py

@@ -14,7 +14,7 @@ from warnings import warn
 import joblib
 from scipy.optimize import least_squares
 
-from pyUSID.processing.comp_utils import recommend_cpu_cores
+from sidpy.proc.comp_utils import recommend_cpu_cores
 from pyUSID.processing.process import Process
 from pyUSID.io.usi_data import USIDataset
 

pycroscopy/analysis/giv_bayesian.py

@@ -12,12 +12,13 @@ Created on Thu Nov 02 11:48:53 2017
 from __future__ import division, print_function, absolute_import, unicode_literals
 
 import numpy as np
-from pyUSID.processing.process import Process
-from pyUSID.processing.comp_utils import parallel_compute
-from pyUSID.io.dtype_utils import stack_real_to_compound
-from pyUSID.io.hdf_utils import write_main_dataset, create_results_group, create_empty_dataset, write_simple_attrs, \
-    print_tree, get_attributes
+from sidpy.proc.comp_utils import parallel_compute
+from sidpy.hdf.dtype_utils import stack_real_to_compound
+from sidpy.hdf.hdf_utils import write_simple_attrs, print_tree, get_attributes
 from pyUSID.io.write_utils import Dimension
+from pyUSID.processing.process import Process
+from pyUSID.io.hdf_utils import write_main_dataset, create_results_group, \
+    create_empty_dataset
 from pyUSID import USIDataset
 from .utils.giv_utils import do_bayesian_inference, bayesian_inference_on_period
 

pycroscopy/analysis/utils/atom_finding.py

@@ -17,8 +17,9 @@ from sklearn.neighbors import KNeighborsClassifier
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
 
-from pyUSID.processing.comp_utils import recommend_cpu_cores
-from pyUSID.io.dtype_utils import stack_real_to_compound
+from sidpy.proc.comp_utils import recommend_cpu_cores
+from sidpy.hdf.dtype_utils import stack_real_to_compound
+
 from ...io.virtual_data import VirtualDataset, VirtualGroup
 from ...io.hdf_writer import HDFwriter
 

pycroscopy/analysis/utils/giv_utils.py

@@ -14,8 +14,8 @@ import numpy as np
 import matplotlib.pyplot as plt
 from scipy.linalg import sqrtm
 
-from pyUSID.io.hdf_utils import get_auxiliary_datasets
-from pyUSID.viz.plot_utils import set_tick_font_size
+from sidpy.hdf.hdf_utils import get_auxiliary_datasets
+from sidpy.viz.plot_utils import set_tick_font_size
 
 
 def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, r_extra=110, gam=0.03, e=10.0, sigma=10., sigmaC=1.,

pycroscopy/processing/cluster.py

@@ -14,15 +14,20 @@ import numpy as np
 import sklearn.cluster as cls
 from scipy.cluster.hierarchy import linkage
 from scipy.spatial.distance import pdist
-from .proc_utils import get_component_slice
+
+from sidpy.hdf.hdf_utils import write_simple_attrs, get_attr
+from sidpy.base.string_utils import format_time
+from sidpy.hdf.dtype_utils import check_dtype, stack_real_to_target_dtype
+from sidpy.proc.comp_utils import parallel_compute
+
 from pyUSID.processing.process import Process
-from pyUSID.processing.comp_utils import parallel_compute
-from pyUSID.io.hdf_utils import reshape_to_n_dims, create_results_group, write_main_dataset, get_attr, \
-    write_simple_attrs, link_h5_obj_as_alias, write_ind_val_dsets
+from pyUSID.io.hdf_utils import reshape_to_n_dims, create_results_group, write_main_dataset, \
+    write_ind_val_dsets
 from pyUSID import USIDataset
-from pyUSID.io.io_utils import format_time
 from pyUSID.io.write_utils import Dimension
-from pyUSID.io.dtype_utils import check_dtype, stack_real_to_target_dtype
+
+from .proc_utils import get_component_slice
+
 
 
 class Cluster(Process):

pycroscopy/processing/decomposition.py

@@ -14,12 +14,14 @@ import time
 import numpy as np
 import sklearn.decomposition as dec
 
+from sidpy.hdf.hdf_utils import write_simple_attrs, get_attr
+from sidpy.base.string_utils import format_time
+from sidpy.hdf.dtype_utils import check_dtype, stack_real_to_target_dtype
+
 from pyUSID.processing.process import Process
-from pyUSID.io.hdf_utils import reshape_to_n_dims, create_results_group, write_main_dataset, get_attr, \
-    write_simple_attrs
+from pyUSID.io.hdf_utils import reshape_to_n_dims, create_results_group, \
+    write_main_dataset
 from pyUSID.io.write_utils import Dimension
-from pyUSID.io.dtype_utils import check_dtype, stack_real_to_target_dtype
-from pyUSID.io.io_utils import format_time
 from pyUSID import USIDataset
 
 

pycroscopy/processing/gmode_utils.py

@@ -15,9 +15,12 @@ from numbers import Number
 import matplotlib.pyplot as plt
 import numpy as np
 from .fft import get_noise_floor, are_compatible_filters, build_composite_freq_filter
+
+from sidpy.hdf.hdf_utils import get_attr
+from sidpy.viz.plot_utils import set_tick_font_size, plot_curves
+
 from pyUSID import USIDataset
-from pyUSID.io.hdf_utils import check_if_main, get_attr, write_main_dataset, create_results_group
-from pyUSID.viz.plot_utils import set_tick_font_size, plot_curves
+from pyUSID.io.hdf_utils import check_if_main, write_main_dataset, create_results_group
 from pyUSID.io.write_utils import Dimension
 
 if sys.version_info.major == 3:

pycroscopy/processing/signal_filter.py

@@ -13,11 +13,15 @@ from __future__ import division, print_function, absolute_import, unicode_litera
 import h5py
 import numpy as np
 from collections import Iterable
-from pyUSID.processing.process import Process
-from pyUSID.processing.comp_utils import parallel_compute
-from pyUSID.io.hdf_utils import create_results_group, write_main_dataset, write_simple_attrs, create_empty_dataset, \
-    write_ind_val_dsets
+
+from sidpy.proc.comp_utils import parallel_compute
+from sidpy.hdf.hdf_utils import write_simple_attrs
+
 from pyUSID.io.write_utils import Dimension
+from pyUSID.io.hdf_utils import create_results_group, write_main_dataset, create_empty_dataset, \
+    write_ind_val_dsets
+from pyUSID.processing.process import Process
+
 from .fft import get_noise_floor, are_compatible_filters, build_composite_freq_filter
 from .gmode_utils import test_filter
 

pycroscopy/processing/svd_utils.py

@@ -14,15 +14,17 @@ import numpy as np
 from sklearn.utils import gen_batches
 from sklearn.utils.extmath import randomized_svd
 
+from sidpy.hdf.reg_ref import get_indices_for_region_ref, create_region_reference
+from sidpy.hdf.hdf_utils import get_attr, write_simple_attrs
+from sidpy.proc.comp_utils import get_available_memory
+from sidpy.base.string_utils import format_time
+from sidpy.hdf.dtype_utils import check_dtype, stack_real_to_target_dtype
+
 from pyUSID.processing.process import Process
 from .proc_utils import get_component_slice
-from pyUSID.io.reg_ref import get_indices_for_region_ref, create_region_reference
-from pyUSID.io.hdf_utils import find_results_groups, \
-    copy_attributes, reshape_to_n_dims, get_attr, write_main_dataset, \
-    create_results_group, write_simple_attrs, create_indexed_group
-from pyUSID.processing.comp_utils import get_available_memory
-from pyUSID.io.io_utils import format_time
-from pyUSID.io.dtype_utils import check_dtype, stack_real_to_target_dtype
+from pyUSID.io.hdf_utils import find_results_groups, copy_attributes, \
+    reshape_to_n_dims, write_main_dataset, create_results_group, \
+    create_indexed_group
 from pyUSID.io.write_utils import Dimension, calc_chunks
 from pyUSID import USIDataset
 

pycroscopy/viz/be_viz_utils.py

@@ -16,13 +16,14 @@ import numpy as np
 from IPython.display import display
 from matplotlib import pyplot as plt
 
-from pyUSID.viz.plot_utils import plot_curves, plot_map_stack, get_cmap_object, plot_map, set_tick_font_size, \
+from sidpy.viz.plot_utils import plot_curves, plot_map_stack, get_cmap_object, plot_map, set_tick_font_size, \
     plot_complex_spectra
-from pyUSID.viz.jupyter_utils import save_fig_filebox_button
+from sidpy.viz.jupyter_utils import save_fig_filebox_button
+from sidpy.hdf.hdf_utils import get_auxiliary_datasets, get_attr
 from ..analysis.utils.be_loop import loop_fit_function
 from ..analysis.utils.be_sho import SHOfunc
-from pyUSID.io.hdf_utils import reshape_to_n_dims, get_auxiliary_datasets, get_sort_order, get_dimensionality, \
-    get_attr, get_source_dataset
+from pyUSID.io.hdf_utils import reshape_to_n_dims, get_sort_order, get_dimensionality, \
+    get_source_dataset
 from pyUSID import USIDataset
 
 

pycroscopy/viz/cluster_utils.py

@@ -18,10 +18,11 @@ from matplotlib import pyplot as plt
 if sys.version_info.major == 3:
     unicode = str
 
-from pyUSID import USIDataset
-from pyUSID.io.hdf_utils import get_attr
-from pyUSID.viz.plot_utils import plot_complex_spectra, plot_map_stack, default_cmap, plot_map, \
+
+from sidpy.hdf.hdf_utils import get_attr
+from sidpy.viz.plot_utils import plot_complex_spectra, plot_map_stack, default_cmap, plot_map, \
     discrete_cmap, plot_line_family, make_scalar_mappable, plot_curves
+from pyUSID import USIDataset
 
 
 def plot_cluster_h5_group(h5_group, labels_kwargs=None, centroids_kwargs=None):

pycroscopy/viz/image_cleaning_utils.py

@@ -11,7 +11,7 @@ import scipy
 from matplotlib import pyplot as plt
 from mpl_toolkits.axes_grid1 import ImageGrid
 
-from pyUSID.viz.plot_utils import plot_map
+from sidpy.viz.plot_utils import plot_map
 
 
 def plot_image_cleaning_results(raw_image, clean_image, stdevs=2, heading='Image Cleaning Results',