Commit 1a82212e authored by ssomnath's avatar ssomnath
Browse files

Importing from sidpy instead of pyUSID wherever appropriate

parent 0e6f0d92
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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.,
......
......@@ -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):
......
......@@ -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
......
......@@ -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:
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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):
......
......@@ -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',
......
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