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Commit bb1d0176 authored by Somnath, Suhas's avatar Somnath, Suhas
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Cleaned documentation 

For io utils and plot utils
parent 009ec563
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pycroscopy/io/io_utils.py
View file @ bb1d0176
......@@ -11,7 +11,7 @@ from time import strftime
from PyQt4 import QtGui
def getTimeStamp():
'''
"""
Teturns the current date and time as a string formatted as:
Year_Month_Dat-Hour_Minute_Second
......@@ -22,12 +22,12 @@ def getTimeStamp():
Returns
---------
String
'''
"""
return strftime('%Y_%m_%d-%H_%M_%S')
def uiGetFile(extension, caption='Select File'):
'''
"""
Presents a File dialog used for selecting the .mat file
and returns the absolute filepath of the selecte file\n
......@@ -42,13 +42,13 @@ def uiGetFile(extension, caption='Select File'):
--------
file_path : String
Absolute path of the chosen file
'''
"""
return QtGui.QFileDialog.getOpenFileName(caption=caption, filter=extension)
def getAvailableMem():
'''
"""
Returns the available memory
Chris Smith -- csmith55@utk.edu
......@@ -61,14 +61,14 @@ def getAvailableMem():
--------
mem : unsigned int
Memory in bytes
'''
"""
from psutil import virtual_memory as vm
mem = vm()
return getattr(mem, 'available')
def recommendCores(num_jobs, requested_cores=None):
'''
"""
Decides the number of cores to use for parallel computing
Parameters
......@@ -82,7 +82,7 @@ def recommendCores(num_jobs, requested_cores=None):
--------
requested_cores : unsigned int
Number of logical cores to use for computation
'''
"""
max_cores = max(1, cpu_count() - 2)
......@@ -103,79 +103,95 @@ def recommendCores(num_jobs, requested_cores=None):
return requested_cores
def complex_to_float(h5_main):
'''
Function to convert a complex HDF5 dataset into a scalar dataset
def complex_to_float(ds_main):
"""
Function to convert a complex ND numpy array or HDF5 dataset into a scalar dataset
Parameters
----------
h5_main: HDF5 Dataset object with a complex datatype
'''
return np.hstack([np.real(h5_main), np.imag(h5_main)])
ds_main : complex ND numpy array or ND HDF5 dataset
Dataset of interest
def compound_to_scalar(h5_main):
'''
Function to convert a compound HDF5 dataset into a scalar dataset
Returns
--------
retval : ND real numpy array
"""
return np.hstack([np.real(ds_main), np.imag(ds_main)])
def compound_to_scalar(ds_main):
"""
Converts a compound ND numpy array or HDF5 dataset into a real scalar dataset
Parameters
----------
h5_main: HDF5 Dataset object with a compound datatype
'''
if isinstance(h5_main, h5py.Dataset):
return np.hstack([np.float32(h5_main[name]) for name in h5_main.dtype.names])
elif isinstance(h5_main, np.ndarray):
return np.hstack([h5_main[name] for name in h5_main.dtype.names])
ds_main : ND numpy array or ND HDF5 dataset object of compound datatype
Dataset of interest
Returns
--------
retval : ND real numpy array
"""
if isinstance(ds_main, h5py.Dataset):
return np.hstack([np.float32(ds_main[name]) for name in ds_main.dtype.names])
elif isinstance(ds_main, np.ndarray):
return np.hstack([ds_main[name] for name in ds_main.dtype.names])
else:
raise TypeError('Datatype {} not supported in compound_to_scalar'.format(type(h5_main)))
raise TypeError('Datatype {} not supported in compound_to_scalar'.format(type(ds_main)))
def check_dtype(h5_main):
'''
def check_dtype(ds_main):
"""
Checks the datatype of the input dataset and provides the appropriate
function calls to convert it to a float
parameter
h5_main -- HDF5 Dataset
Parameters
------------
ds_main : HDF5 Dataset
Dataset of interest
returns
Returns
-------
func -- function call that will convert the dataset to a float
is_complex -- Boolean, is the input dataset complex
is_compound -- Boolean, is the input dataset compound
n_features -- Unsigned integer, the length of the 2nd dimension of
the data after func is called on it
n_samples -- Unsigned integer, the length of the 1st dimension of
the data
type_mult -- Unsigned integer, multiplier that converts from the
typesize of the input dtype to the typesize of the data
after func is run on it
'''
func : function
function that will convert the dataset to a float
is_complex : Boolean
is the input dataset complex?
is_compound : Boolean
is the input dataset compound?
n_features : Unsigned integer, the length of the 2nd dimension of
the data after func is called on it
n_samples : Unsigned integer
the length of the 1st dimension of the data
type_mult : Unsigned integer
multiplier that converts from the typesize of the input dtype to the
typesize of the data after func is run on it
"""
is_complex = False
is_compound = False
in_dtype = h5_main.dtype
new_dtype = h5_main.dtype
n_samples, n_features = h5_main.shape
if h5_main.dtype in [np.complex64, np.complex128, np.complex]:
in_dtype = ds_main.dtype
new_dtype = ds_main.dtype
n_samples, n_features = ds_main.shape
if ds_main.dtype in [np.complex64, np.complex128, np.complex]:
is_complex = True
new_dtype = np.real(h5_main[0, 0]).dtype
new_dtype = np.real(ds_main[0, 0]).dtype
type_mult = new_dtype.itemsize * 2
func = complex_to_float
n_features *= 2
elif len(h5_main.dtype) > 1:
'''
elif len(ds_main.dtype) > 1:
"""
Some form of compound datatype is in use
We only support real scalars for the component types at the current time
'''
"""
is_compound = True
new_dtype = np.float32
type_mult = len(in_dtype) * new_dtype(0).itemsize
func = compound_to_scalar
n_features *= len(in_dtype)
else:
if h5_main.dtype not in [np.float32, np.float64]:
if ds_main.dtype not in [np.float32, np.float64]:
new_dtype = np.float32
else:
new_dtype = h5_main.dtype.type
new_dtype = ds_main.dtype.type
type_mult = new_dtype(0).itemsize
......
pycroscopy/viz/plot_utils.py
View file @ bb1d0176
......@@ -130,7 +130,7 @@ def plotLoops(excit_wfm, h5_loops, h5_pos=None, central_resp_size=None,
def plotSHOMaps(sho_maps, map_names, stdevs=2, title='', save_path=None):
'''
"""
Plots the SHO quantity maps for a single UDVS step
Parameters
......@@ -149,7 +149,7 @@ def plotSHOMaps(sho_maps, map_names, stdevs=2, title='', save_path=None):
Returns
----------
None
'''
"""
fig,axes=plt.subplots(ncols=3, nrows=2, sharex=True, figsize=(15, 10))
for index, ax_hand, data_mat, qty_name in zip(range(len(map_names)), axes.flat, sho_maps, map_names):
......@@ -170,7 +170,7 @@ def plotSHOMaps(sho_maps, map_names, stdevs=2, title='', save_path=None):
def plotVSsnapshots(resp_mat, title='', stdevs=2, save_path=None):
'''
"""
Plots the spatial distribution of the response at evenly spaced UDVS steps
Parameters
......@@ -187,7 +187,7 @@ def plotVSsnapshots(resp_mat, title='', stdevs=2, save_path=None):
Returns
----------
None
'''
"""
num_udvs = resp_mat.shape[2]
if num_udvs >= 9:
......@@ -227,7 +227,7 @@ def plotVSsnapshots(resp_mat, title='', stdevs=2, save_path=None):
def plotSpectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='Step', stdevs=2,
show_colorbar=True):
'''
"""
Plots the provided spectrograms from SVD V vector
Parameters:
......@@ -250,7 +250,7 @@ def plotSpectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='St
Returns:
---------
fig, axes
'''
"""
import matplotlib.pyplot as plt
fig_h, fig_w = (4, 4 + show_colorbar * 1.00)
p_rows = int(np.ceil(np.sqrt(num_comps)))
......@@ -277,7 +277,7 @@ def plotSpectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='St
###############################################################################
def plotBEspectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='UDVS Step', stdevs=2):
'''
"""
Plots the provided spectrograms from SVD V vector
Parameters:
......@@ -300,7 +300,7 @@ def plotBEspectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='
Returns:
---------
fig, axes
'''
"""
fig201, axes201 = plt.subplots(2, num_comps, figsize=(4 * num_comps, 8))
fig201.subplots_adjust(hspace=0.4, wspace=0.4)
fig201.canvas.set_window_title(title)
......@@ -325,7 +325,7 @@ def plotBEspectrograms(eigenvectors, num_comps=4, title='Eigenvectors', xlabel='
###############################################################################
def plotBEeigenvectors(eigenvectors, num_comps=4, xlabel=''):
'''
"""
Plots the provided spectrograms from SVD V vector
Parameters:
......@@ -348,7 +348,7 @@ def plotBEeigenvectors(eigenvectors, num_comps=4, xlabel=''):
Returns:
---------
fig, axes
'''
"""
funcs = [np.abs, np.angle]
labels = ['Amplitude', 'Phase']
......@@ -372,7 +372,7 @@ def plotBEeigenvectors(eigenvectors, num_comps=4, xlabel=''):
###############################################################################
def plotBELoops(xaxis, xlabel, amp_mat, phase_mat, num_comps, title=None):
'''
"""
Plots the provided loops from the SHO. Replace / merge with function in BESHOUtils
Parameters:
......@@ -393,7 +393,7 @@ def plotBELoops(xaxis, xlabel, amp_mat, phase_mat, num_comps, title=None):
Returns:
---------
fig, axes
'''
"""
fig201, axes201 = plt.subplots(2, num_comps, figsize=(4 * num_comps, 6))
fig201.subplots_adjust(hspace=0.4, wspace=0.4)
fig201.canvas.set_window_title(title)
......@@ -416,7 +416,7 @@ def plotBELoops(xaxis, xlabel, amp_mat, phase_mat, num_comps, title=None):
###############################################################################
def plotScree(S, title='Scree'):
'''
"""
Plots the S or scree
Parameters:
......@@ -427,7 +427,7 @@ def plotScree(S, title='Scree'):
Returns:
---------
fig, axes
'''
"""
fig203 = plt.figure(figsize=(6.5, 6))
axes203 = fig203.add_axes([0.1, 0.1, .8, .8]) # left, bottom, width, height (range 0 to 1)
axes203.loglog(np.arange(len(S)) + 1, S, 'b', marker='*')
......@@ -444,7 +444,7 @@ def plotScree(S, title='Scree'):
###############################################################################
def plotLoadingMaps(loadings, num_comps=4, stdevs=2, colormap='jet', show_colorbar=True):
'''
"""
Plots the provided loading maps
Parameters:
......@@ -463,7 +463,7 @@ def plotLoadingMaps(loadings, num_comps=4, stdevs=2, colormap='jet', show_colorb
Returns:
---------
fig, axes
'''
"""
fig_h, fig_w = (4, 4 + show_colorbar * 1.00)
p_rows = int(np.ceil(np.sqrt(num_comps)))
p_cols = int(np.floor(num_comps / p_rows))
......@@ -496,7 +496,7 @@ def plotLoadingMaps(loadings, num_comps=4, stdevs=2, colormap='jet', show_colorb
def plotKMeansResults(label_mat, cluster_centroids, spec_val=None, cmap=plt.cm.jet,
spec_label='Spectroscopic Value', resp_label='Response'):
'''
"""
label_mat : 2D int numpy array or h5py.Dataset object
Spatial map of cluster labels structured as [rows, cols]
cluster_centroids : 2D array or h5py.Dataset object
......@@ -511,7 +511,7 @@ def plotKMeansResults(label_mat, cluster_centroids, spec_val=None, cmap=plt.cm.j
Label to use for X axis on cluster centroid plot
resp_label : String (Optional. Default = 'Response')
Label to use for Y axis on cluster centroid plot
'''
"""
def __plotCentroids(centroids, ax, spec_val, spec_label, y_label, cmap, title=None):
num_clusters = centroids.shape[0]
......@@ -547,9 +547,9 @@ def plotKMeansResults(label_mat, cluster_centroids, spec_val=None, cmap=plt.cm.j
num_clusters = cluster_centroids.shape[0]
if isinstance(label_mat, h5py.Dataset):
'''
"""
Reshape label_mat based on linked positions
'''
"""
pos = label_mat.file[label_mat.attrs['Position_Indices']]
nx = len(np.unique(pos[:, 0]))
ny = len(np.unique(pos[:, 1]))
......@@ -574,7 +574,7 @@ def plotKMeansResults(label_mat, cluster_centroids, spec_val=None, cmap=plt.cm.j
def plotKMeansClusters(label_mat, cluster_centroids,
num_cluster=4):
'''
"""
Plots the provided label mat and centroids
from KMeans clustering
......@@ -590,7 +590,7 @@ def plotKMeansClusters(label_mat, cluster_centroids,
Returns:
---------
fig
'''
"""
if num_cluster < 5:
......@@ -645,7 +645,7 @@ def plotKMeansClusters(label_mat, cluster_centroids,
def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full', last=None,
sort_type='distance', sort_mode=True):
'''
"""
Creates and plots the dendrograms for the given label_mat and
eigenvalues
......@@ -688,7 +688,7 @@ def plotClusterDendrograms(label_mat, e_vals, num_comp, num_cluster, mode='Full'
Returns
---------
fig
'''
"""
if mode == 'Truncated' and not last:
warn('Warning: Truncated dendrograms requested, but no last cluster given. Reverting to full dendrograms.')
mode = 'Full'
......
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