Commit df724721 authored by Unknown's avatar Unknown
Browse files

Minor Docstring cleanups

parent 368c3fb2
...@@ -28,6 +28,7 @@ class Fit_Methods(object): ...@@ -28,6 +28,7 @@ class Fit_Methods(object):
Parameters Parameters
----------- -----------
freq_vector : numpy.ndarray
args : list or tuple args : list or tuple
SHO parameters=(Amp,w0,Q,phi,vector). vector: 1D np.array of frequency values. SHO parameters=(Amp,w0,Q,phi,vector). vector: 1D np.array of frequency values.
Amp: amplitude. Amp: amplitude.
......
...@@ -89,7 +89,7 @@ def gauss2d(X, Y, *parms, **kwargs): ...@@ -89,7 +89,7 @@ def gauss2d(X, Y, *parms, **kwargs):
X, Y : the x and y matrix values from the call "X, Y = np.meshgrid(x,y)" where x and y are X, Y : the x and y matrix values from the call "X, Y = np.meshgrid(x,y)" where x and y are
defined by x = np.arange(-width/2,width/2) and y = np.arange(-height/2,height/2). defined by x = np.arange(-width/2,width/2) and y = np.arange(-height/2,height/2).
params: List of 7 parameters defining the gaussian. parms: List of 7 parameters defining the gaussian.
The parameters are [A, x0, y0, sigma_x, sigma_y, theta, background] The parameters are [A, x0, y0, sigma_x, sigma_y, theta, background]
A : amplitude A : amplitude
x0: x position x0: x position
...@@ -497,8 +497,6 @@ class Gauss_Fit(object): ...@@ -497,8 +497,6 @@ class Gauss_Fit(object):
Parameters Parameters
---------- ----------
None
Returns Returns
------- -------
......
...@@ -125,8 +125,8 @@ def SHOfastGuess(w_vec, resp_vec, qual_factor=200): ...@@ -125,8 +125,8 @@ def SHOfastGuess(w_vec, resp_vec, qual_factor=200):
Quality factor of the SHO peak Quality factor of the SHO peak
Returns Returns
-------
retval : 1D numpy array retval : 1D numpy array
---------
SHO fit parameters arranged as [amplitude, frequency, quality factor, phase] SHO fit parameters arranged as [amplitude, frequency, quality factor, phase]
""" """
amp_vec = abs(resp_vec) amp_vec = abs(resp_vec)
......
...@@ -30,7 +30,7 @@ def uiGetFile(filter='H5 file (*.h5)', caption='Select File'): ...@@ -30,7 +30,7 @@ def uiGetFile(filter='H5 file (*.h5)', caption='Select File'):
Parameters Parameters
---------- ----------
extension : String or list of strings filter : String or list of strings
file extensions to look for file extensions to look for
caption : (Optional) String caption : (Optional) String
Title for the file browser window Title for the file browser window
...@@ -84,7 +84,6 @@ def getTimeStamp(): ...@@ -84,7 +84,6 @@ def getTimeStamp():
Parameters Parameters
---------- ----------
None
Returns Returns
------- -------
...@@ -101,7 +100,6 @@ def getAvailableMem(): ...@@ -101,7 +100,6 @@ def getAvailableMem():
Parameters Parameters
---------- ----------
None
Returns Returns
------- -------
......
...@@ -91,13 +91,6 @@ class MicroDataGroup(MicroData): ...@@ -91,13 +91,6 @@ class MicroDataGroup(MicroData):
""" """
Return the tree structure given by MicroDataGroup. Return the tree structure given by MicroDataGroup.
Parameters
----------
None
Returns
-------
None
""" """
def __tree(child, parent): def __tree(child, parent):
......
...@@ -341,6 +341,9 @@ def generatePlotGroups(h5_main, hdf, mean_resp, folder_path, basename, max_resp= ...@@ -341,6 +341,9 @@ def generatePlotGroups(h5_main, hdf, mean_resp, folder_path, basename, max_resp=
do_histogram : Boolean (Optional. Default = False) do_histogram : Boolean (Optional. Default = False)
Whether or not to generate hisograms. Whether or not to generate hisograms.
Caution - Histograms can take a fair amount of time to compute. Caution - Histograms can take a fair amount of time to compute.
debug : Boolean, Optional
If True, then extra debug statements are printed.
Default False
""" """
grp = h5_main.parent grp = h5_main.parent
...@@ -1287,9 +1290,15 @@ class BEHistogram(): ...@@ -1287,9 +1290,15 @@ class BEHistogram():
Parameters Parameters
---------- ----------
h5_path : hdf5 reference to Main_Dataset h5_main : hdf5.Dataset
max_response : list
min_response : list
max_mem_mb : int
max_bins : int
debug : bool
Outputs: Returns
-------
""" """
...@@ -1353,13 +1362,13 @@ class BEHistogram(): ...@@ -1353,13 +1362,13 @@ class BEHistogram():
---------- ----------
h5_main : HDF5 Dataset object h5_main : HDF5 Dataset object
Dataset to be historammed Dataset to be historammed
activ_spec_steps : numpy array active_spec_steps : numpy array
active spectral steps in the current plot group active spectral steps in the current plot group
max_response : numpy array max_response : numpy array
maximum amplitude at each pixel maximum amplitude at each pixel
min_response : numpy array min_response : numpy array
minimum amplitude at each pixel minimum amplitude at each pixel
max_mem : Unsigned integer max_mem_mb : Unsigned integer
maximum number of Mb allowed for use. Used to calculate the maximum number of Mb allowed for use. Used to calculate the
number of pixels to load in a chunk number of pixels to load in a chunk
max_bins : integer max_bins : integer
......
...@@ -88,6 +88,7 @@ def unnest_parm_dicts(image_parms, prefix=''): ...@@ -88,6 +88,7 @@ def unnest_parm_dicts(image_parms, prefix=''):
Parameters Parameters
---------- ----------
image_parms : dict image_parms : dict
prefix : str
Returns Returns
------- -------
......
...@@ -54,6 +54,9 @@ class MovieTranslator(Translator): ...@@ -54,6 +54,9 @@ class MovieTranslator(Translator):
start_image : int, optional start_image : int, optional
Integer denoting which image in the file path should be considered the starting Integer denoting which image in the file path should be considered the starting
point. Default is 0, start with the first image on the list. point. Default is 0, start with the first image on the list.
image_type : str, optional
File extension of images to load. Used to filter out other files in the same
directory. Default .tif
Returns Returns
---------- ----------
......
...@@ -811,7 +811,7 @@ def return_pos(file_in_h5, img_num): ...@@ -811,7 +811,7 @@ def return_pos(file_in_h5, img_num):
image_path = "/Frame_%04i/Channel_Finished" % (img_num) image_path = "/Frame_%04i/Channel_Finished" % (img_num)
type_ref = type(main_h5_handle.get(image_path)) type_ref = type(main_h5_handle.get(image_path))
temp = 1 temp = 1
x = -1; x = -1
while temp: while temp:
x = x + 1 x = x + 1
image_path = "%s/Filter_Step_%04i" % (image_path, x) image_path = "%s/Filter_Step_%04i" % (image_path, x)
...@@ -890,7 +890,7 @@ def run_PCA_atoms(file_in_h5, img_num, box_width): ...@@ -890,7 +890,7 @@ def run_PCA_atoms(file_in_h5, img_num, box_width):
box_width <= pos[k1, 1].round() <= len(img[0, :]) - box_width): box_width <= pos[k1, 1].round() <= len(img[0, :]) - box_width):
sel_vec[k1] = 1 sel_vec[k1] = 1
new_pos.append(pos[k1, :]) new_pos.append(pos[k1, :])
vector = img[pos[k1, 0] - box_width:pos[k1, 0] + box_width, pos[k1, 1] - box_width:pos[k1, 1] + box_width]; vector = img[pos[k1, 0] - box_width:pos[k1, 0] + box_width, pos[k1, 1] - box_width:pos[k1, 1] + box_width]
img_vectors.append(vector.reshape([(box_width * 2) ** 2])) img_vectors.append(vector.reshape([(box_width * 2) ** 2]))
new_pos = array(new_pos) new_pos = array(new_pos)
......
...@@ -136,7 +136,12 @@ def noiseBandFilter(num_pts, samp_rate, freqs, freq_widths, show_plots=False): ...@@ -136,7 +136,12 @@ def noiseBandFilter(num_pts, samp_rate, freqs, freq_widths, show_plots=False):
Target frequencies as unsigned ints Target frequencies as unsigned ints
freq_widths : 1D array or list freq_widths : 1D array or list
Width around the target frequency that should be set to 0\n Width around the target frequency that should be set to 0\n
Note: sampRate, freqs, freq_widths have same units - eg MHz show_plots : bool
If True, plots will be displayed during calculation. Default False
Note
----
sampRate, freqs, freq_widths have same units - eg MHz
Returns Returns
------- -------
......
...@@ -39,6 +39,8 @@ def buildHistogram(x_hist, data_mat, N_x_bins, N_y_bins, weighting_vec=1, min_re ...@@ -39,6 +39,8 @@ def buildHistogram(x_hist, data_mat, N_x_bins, N_y_bins, weighting_vec=1, min_re
func : function func : function
function to be used to bin data_vec. All functions should take as input data_vec. function to be used to bin data_vec. All functions should take as input data_vec.
Arguments should be passed properly to func. This has not been heavily tested. Arguments should be passed properly to func. This has not been heavily tested.
debug : bool, optional
If True, extra debugging statements are printed. Default False
Returns Returns
------- -------
......
...@@ -111,13 +111,6 @@ class Process(object): ...@@ -111,13 +111,6 @@ class Process(object):
Parameters Parameters
---------- ----------
func func
strategy: string
Default is 'Wavelet_Peaks'.
Can be one of ['wavelet_peaks', 'relative_maximum', 'gaussian_processes'].
For updated list, run GuessMethods.methods
options: dict
Default {"peaks_widths": np.array([10,200])}}.
Dictionary of options passed to strategy. For more info see GuessMethods documentation.
kwargs: kwargs:
processors: int processors: int
......
...@@ -558,14 +558,14 @@ def plot_complex_loop_stack(loop_stack, x_axis, heading='BE Loops', subtitle='Ei ...@@ -558,14 +558,14 @@ def plot_complex_loop_stack(loop_stack, x_axis, heading='BE Loops', subtitle='Ei
Loops rearranged as - [component, points] Loops rearranged as - [component, points]
x_axis : 1D real numpy array x_axis : 1D real numpy array
The vector to plot against The vector to plot against
heading : str
Title to plot above everything else
subtitle : str
Subtile to of Figure
num_comps : int num_comps : int
Number of components to plot Number of components to plot
title : String x_label : str
Title to plot above everything else
x_label : String
Label for x axis Label for x axis
stdevs : int
Number of standard deviations to consider for plotting
Returns Returns
--------- ---------
...@@ -601,6 +601,8 @@ def plotScree(scree, title='Scree'): ...@@ -601,6 +601,8 @@ def plotScree(scree, title='Scree'):
------------- -------------
scree : 1D real numpy array scree : 1D real numpy array
The scree vector from SVD The scree vector from SVD
title : str
Figure title. Default Scree
Returns Returns
--------- ---------
...@@ -637,6 +639,10 @@ def plot_map_stack(map_stack, num_comps=9, stdevs=2, color_bar_mode=None, evenly ...@@ -637,6 +639,10 @@ def plot_map_stack(map_stack, num_comps=9, stdevs=2, color_bar_mode=None, evenly
Number of standard deviations to consider for plotting Number of standard deviations to consider for plotting
color_bar_mode : String, Optional color_bar_mode : String, Optional
Options are None, single or each. Default None Options are None, single or each. Default None
evenly_spaced : bool
Default False
reverse_dims : Boolean (Optional)
Set this to False to accept data structured as [component, rows, cols]
title : String or list of strings title : String or list of strings
The titles for each of the plots. The titles for each of the plots.
If a single string is provided, the plot titles become ['title 01', title 02', ...]. If a single string is provided, the plot titles become ['title 01', title 02', ...].
...@@ -650,8 +656,6 @@ def plot_map_stack(map_stack, num_comps=9, stdevs=2, color_bar_mode=None, evenly ...@@ -650,8 +656,6 @@ def plot_map_stack(map_stack, num_comps=9, stdevs=2, color_bar_mode=None, evenly
Multipliers for the axis padding between plots in the stack. Padding is calculated as Multipliers for the axis padding between plots in the stack. Padding is calculated as
(pad_mult[0]*fig_mult[1], pad_mult[1]*fig_mult[0]) for the width and height padding respectively. (pad_mult[0]*fig_mult[1], pad_mult[1]*fig_mult[0]) for the width and height padding respectively.
Default (0.1, 0.07) Default (0.1, 0.07)
reverse_dims : Boolean (Optional)
Set this to False to accept data structured as [component, rows, cols]
kwargs : dictionary kwargs : dictionary
Keyword arguments to be passed to either matplotlib.pyplot.figure, mpl_toolkits.axes_grid1.ImageGrid, or Keyword arguments to be passed to either matplotlib.pyplot.figure, mpl_toolkits.axes_grid1.ImageGrid, or
pycroscopy.vis.plot_utils.plot_map. See specific function documentation for the relavent options. pycroscopy.vis.plot_utils.plot_map. See specific function documentation for the relavent options.
...@@ -1286,7 +1290,6 @@ def plot_image_cleaning_results(raw_image, clean_image, stdevs=2, heading='Image ...@@ -1286,7 +1290,6 @@ def plot_image_cleaning_results(raw_image, clean_image, stdevs=2, heading='Image
raw_image raw_image
clean_image clean_image
stdevs stdevs
color_bar_mode
fig_mult fig_mult
fig_args fig_args
heading heading
......
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