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dabam.py
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dabam.py
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"""
dabam: (dataBase for metrology)
python module for processing remote files containing the results of metrology measurements on X-ray mirrors
classes:
* dabam
main functions:
* cdf (calculate antiderivative function)
* psd (calculate power spectral density)
* write_shadowSurface (writes file with a mesh for SHADOW)
* func_ellipse_slopes evaluates the ellipse slopes profile equation
MODIFICATION HISTORY:
* 20130902 srio@esrf.eu, written
* 20131109 srio@esrf.eu, added command line arguments, access metadata
* 20151103 srio@esrf.eu, restructured to OO
* 20151118 srio@esrf.eu, cleaned and tested
* 20190731 srio@lbl.gov, updated version, allows reading external files, change server, etc.
"""
__author__ = "Manuel Sanchez del Rio"
__contact__ = "srio@esrf.eu"
import traceback
__copyright = "ESRF, 2013-2015; LBNL, 2019"
import numpy
import copy
# to manage input parameters from command-line argument
import sys
import argparse
import json
import os
from io import StringIO
from urllib.request import urlopen
default_server = "https://raw.githubusercontent.com/oasys-kit/DabamFiles/main/"
class dabam(object):
"""
Constructor.
"""
def __init__(self):
self.description="dabam.py: python program to access and evaluate DAta BAse for Metrology (DABAM) files. See https://github.com/oasys-kit/DabamFiles"
self.is_remote_access = True
self.server = default_server
self.server_local = ""
self.inputs = {
'entryNumber':1, # 'an integer indicating the DABAM entry number'
'silent':False, # 'Silent mode. Default is No'
'localFileRoot':None, # 'Define the name of local DABAM file root (<name>.dat for data, <name>.txt for metadata).'
'outputFileRoot':"", # 'Define the root for output files. Default is "", so no output files'
'setDetrending':-2, # 'Detrending: if >0 is the polynomial degree, -1=skip, -2=read from metadata DETRENDING, -3=ellipse(optimized) -4=ellipse(design)'
'detrendingWindowFactor': 1.0, # 'if setDetrending>0, this is the window covering for the fit (1.0 is full window)'
'resetZeroHeight': 0, # 'reset zero in heights profile 0=No, 1=to heihjty minimum, 2=to center'
'nbinS':101, # 'number of bins of the slopes histogram in rads. '
'nbinH':101, # 'number of bins heights histogram in m. '
'shadowCalc':False, # 'Write file with mesh for SHADOW.'
'shadowNy':-1, # 'For SHADOW file, the number of points along Y (length). If negative, use the profile points. '
'shadowNx':11, # 'For SHADOW file, the number of points along X (width). '
'shadowWidth':6.0, # 'For SHADOW file, the surface dimension along X (width) in cm.'
'shadowFactor': 100.0, # 'For SHADOW file, the factor from m to user unit (e.g. 100 for cm) '
'multiply':1.0, # 'Multiply input profile (slope or height) by this number (to play with StDev values). '
'oversample':0.0, # 'Oversample factor for abscissas. Interpolate profile foor a new one with this factor times npoints'
'useHeightsOrSlopes':-1, # 'Force calculations using profile heights (0) or slopes (1). Overwrites FILE_FORMAT keyword. Default=-1 (like FILE_FORMAT)'
'useAbscissasColumn':-1, # 'Use abscissas column index. Defaut=-1 use the metadata COLUMN_INDEX_ABSCISSAS or 0 if undefined''
'useOrdinatesColumn':-1, # 'Use ordinates column index. Defaut=-1 use the metadata COLUMN_INDEX_ORDINATES or 1 if undefined'
'plot':None, # plot data
# 'runTests':False, # run tests cases
'summary':False, # get summary of DABAM profiles
}
#to load profiles: TODO: rename some variables to more meaningful names
self.metadata = None # metadata
self.rawdata = None # raw datafile
self.y = None # abscissa along the mirror
self.zSlopesUndetrended = None # undetrended slope profile
self.zSlopes = None # detrended slope profile
self.zHeightsUndetrended = None # undetrended heights profile
self.zHeights = None # detrended heights profile
self.coeffs = None # information on detrending (polynomial coeffs)
self.f = None # frequency of Power Spectral Density
self.psdHeights = None # Power Spectral Density of Heights profile
self.psdSlopes = None # Power Spectral Density of slopes profile
self.csdHeights = None # Antiderivative of PDF of Heights profile
self.csdSlopes = None # Antiderivative of PDF of Slopes profile
self.histoSlopes = None # to store slopes histogram
self.histoHeights = None # to store heights histogram
self.momentsSlopes = None # to store moments of the slopes profile
self.momentsHeights = None # to store moments of the heights profile
self.powerlaw = {"hgt_pendent":None, "hgt_shift":None, "slp_pendent":None, "slp_shift":None,
"index_from":None,"index_to":None} # to store a dictionary with the results of fitting the PSDs
@classmethod
def initialize_from_entry_number(cls, entry_number):
"""
Initialize dabax instance with a given profile number.
Parameters
----------
entry_number : int
The dabax profile number.
Returns
-------
a dabax instance
"""
dm = dabam()
dm.load(entry_number)
return dm
@classmethod
def initialize_from_local_server(cls, entry, server=None):
"""
Initialize dabax instance with a given profile number in given server.
Parameters
----------
entry : int
The dabax profile number.
server : str
The server URL or file name.
Returns
-------
a dabax instance.
"""
dm0 = dabam()
dm0.is_remote_access = False
if server is not None:
dm0.set_server(server)
dm0.set_input_entryNumber(entry)
dm0.load()
return dm0
@classmethod
def initialize_from_external_data(cls, input,
column_index_abscissas=0,
column_index_ordinates=1,
skiprows=1,
useHeightsOrSlopes=0,
to_SI_abscissas=1.0,
to_SI_ordinates=1.0,
detrending_flag=-1,
detrending_window_factor=1.0,
reset_zero_height=0, # 0=None, 1=to minimum, 2=to center
):
"""
Returns a dabax instance initialized with external data.
Parameters
----------
input : numpy array
The numpy array with the abscissas and profile heights or slopes.
column_index_abscissas : int, optional
Index of the column with the abscissas.
column_index_ordinates : int, optional
Index of the column with the ordinates.
skiprows : int, optional
Number of rows to skip.
useHeightsOrSlopes : int, optional
The ordinates are: 0=Heights, or 1=Slopes.
to_SI_abscissas : float, optional
The conversion factor from abscissas' units to SI units.
to_SI_ordinates : float, optional
The conversion factor from ordinates' units to SI units.
detrending_flag : int, optional
if >0 is the polynomial degree, -1=skip, -2=read from metadata DETRENDING, -3=ellipse(optimized) -4=ellipse(design).
detrending_window_factor : float, optional
if detrending_flag>0, this is the window covering for the fit (1.0 is full window).
reset_zero_height : int, optional
if 1, resets the minimum value of the height profile to zero.
Returns
-------
instance of dabax.
"""
dm = dabam()
dm.is_remote_access = False
dm.rawdata = numpy.loadtxt(input, skiprows=skiprows)
dm.set_input_useAbscissasColumn(column_index_abscissas)
dm.set_input_useOrdinatesColumn(column_index_ordinates)
dm.set_input_localFileRoot("<none>") # filename.rsplit( ".", 1 )[ 0 ])
dm.set_input_entryNumber(-1)
dm.set_input_multiply(1.0)
dm.set_input_oversample(0.0)
# dm.set_input_setDetrending(-1)
dm.set_input_useHeightsOrSlopes(useHeightsOrSlopes)
# minimalist metadata
dm.metadata = {}
if useHeightsOrSlopes == 0:
dm.metadata["FILE_FORMAT"] = 2
elif useHeightsOrSlopes:
dm.metadata["FILE_FORMAT"] = 1
dm.metadata["FILE_HEADER_LINES"] = skiprows
dm.metadata["X1_FACTOR"] = to_SI_abscissas
for i in range(1, dm.rawdata.shape[1]):
dm.metadata["Y%d_FACTOR" % i] = to_SI_ordinates
dm.metadata["COLUMN_INDEX_ABSCISSAS"] = column_index_abscissas
dm.metadata["COLUMN_INDEX_ORDINATES"] = column_index_ordinates
dm.metadata["DETRENDING"] = detrending_flag
dm.set_input_setDetrending(detrending_flag)
dm.set_input_detrendingWindowFactor(detrending_window_factor)
dm.set_input_resetZeroHeight(reset_zero_height)
dm.make_calculations()
return dm
#
#setters (recommended to use setters for changing input and not setting directly the value in self.inputs,
# because python does not give errors if the key does not exist but create a new one!)
#
@classmethod
def get_default_server(cls):
"""
gets the address of the default server.
Returns
-------
str
Server address.
"""
return default_server
def set_default_server(self):
"""
Defines the current server as the default server.
"""
self.set_server(default_server)
def set_server(self, server):
"""
Sets current server tyo a given address.
Parameters
----------
server : str
The server address.
"""
if server.find("//") >=0:
self.is_remote_access = True
self.server = server
else:
self.is_remote_access = False
self.server_local = server
def get_server(self, directory):
#todo: why directory?
"""
Returns the address of the current server.
Parameters
----------
directory : ? [todo: fix code]
Returns
-------
str
Setver address.
"""
if self.is_remote_access:
return self.server_local
else:
return self.server_local
def reset(self):
"""
Reset the dabax instance to default one.
"""
self.__init__()
#variables
def set_input_entryNumber(self, value):
"""
Sets the current profile number.
Parameters
----------
value : int
The profile number.
"""
self.inputs["entryNumber"] = value
def set_input_silent(self, value):
"""
Sets the input "silent" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["silent"] = value
def set_input_localFileRoot(self,value):
"""
Sets the input "localFileRoot" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["localFileRoot"] = value
if value is not None:
self.is_remote_access = False
def set_input_outputFileRoot(self,value):
"""
Sets the input "outputFileRoot" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["outputFileRoot"] = value
def set_input_setDetrending(self,value):
"""
Sets the input "setDetrending" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["setDetrending"] = value
def set_input_detrendingWindowFactor(self,value):
"""
Sets the input "detrendingWindowFactor" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["detrendingWindowFactor"] = value
def set_input_resetZeroHeight(self,value):
"""
Sets the input "resetZeroHeight" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["resetZeroHeight"] = value
def set_input_nbinS(self,value):
"""
Sets the input "nbinS" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["nbinS"] = value
def set_input_nbinH(self,value):
"""
Sets the input "nbinH" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["nbinH"] = value
def set_input_shadowCalc(self,value):
"""
Sets the input "shadowCalc" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["shadowCalc"] = value
def set_input_shadowNy(self,value):
"""
Sets the input "shadowNy" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["shadowNy"] = value
def set_input_shadowNx(self,value):
"""
Sets the input "shadowNx" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["shadowNx"] = value
def set_input_shadowWidth(self,value):
"""
Sets the input "shadowWidth" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["shadowWidth"] = value
def set_input_shadowFactor(self,value):
"""
Sets the input "shadowFactor" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["shadowFactor"] = value
def set_input_multiply(self,value):
"""
Sets the input "multiply" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["multiply"] = value
def set_input_oversample(self,value):
"""
Sets the input "oversample" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["oversample"] = value
def set_input_useHeightsOrSlopes(self,value):
"""
Sets the input "useHeightsOrSlopes" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["useHeightsOrSlopes"] = value
def set_input_useAbscissasColumn(self,value):
"""
Sets the input "useAbscissasColumn" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["useAbscissasColumn"] = value
def set_input_useOrdinatesColumn(self,value):
"""
Sets the input "useOrdinatesColumn" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["useOrdinatesColumn"] = value
def set_input_plot(self,value):
"""
Sets the input "plot" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["plot"] = value
# def set_input_runTests(self,value):
# self.inputs["runTests"] = value
def set_input_summary(self,value):
"""
Sets the input "summary" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["summary"] = value
# a shortcut (frequent usage)
def set_entry(self,value):
"""
Sets the input "entryNumber" key to a given value.
Parameters
----------
value
The value.
"""
self.inputs["entryNumber"] = value
#others
def set_inputs_from_dictionary(self, dict):
"""
Sets the input keys to given values.
Parameters
----------
dict : dictionary
A dictionary with the values to change.
"""
try:
self.set_input_entryNumber ( dict["entryNumber"] )
self.set_input_silent ( dict["silent"] )
self.set_input_localFileRoot ( dict["localFileRoot"] )
self.set_input_outputFileRoot ( dict["outputFileRoot"] )
self.set_input_setDetrending ( dict["setDetrending"] )
self.set_input_detrendingWindowFactor ( dict["detrendingWindowFactor"] )
self.set_input_resetZeroHeight ( dict["resetZeroHeight"] )
self.set_input_nbinS ( dict["nbinS"] )
self.set_input_nbinH ( dict["nbinH"] )
self.set_input_shadowCalc ( dict["shadowCalc"] )
self.set_input_shadowNy ( dict["shadowNy"] )
self.set_input_shadowNx ( dict["shadowNx"] )
self.set_input_shadowWidth ( dict["shadowWidth"] )
self.set_input_shadowFactor ( dict["shadowFactor"] )
self.set_input_multiply ( dict["multiply"] )
self.set_input_oversample ( dict["oversample"] )
self.set_input_useHeightsOrSlopes ( dict["useHeightsOrSlopes"] )
self.set_input_useAbscissasColumn ( dict["useAbscissasColumn"] )
self.set_input_useOrdinatesColumn ( dict["useOrdinatesColumn"] )
self.set_input_plot ( dict["plot"] )
# self.set_input_runTests ( dict["runTests"] )
self.set_input_summary ( dict["summary"] )
except:
raise Exception("Failed setting dabam input parameters from dictionary")
#
# tools
#
def is_remote_access(self):
"""
Returns
-------
boolean
True is the access is remote (URL).
"""
return self.is_remote_access
def set_remote_access(self):
"""
Sets the acces to be remote.
"""
self.is_remote_access = True
#
#getters
#
def get_input_value(self, key):
"""
Parameters
----------
key : str
key value
Returns
-------
The input corresponding to that key.
"""
try:
return self.inputs[key]
except:
print("****get_input_value: Error returning value for key=%s"%(key))
return None
def get_inputs_as_dictionary(self):
"""
Returns
-------
dict
The inputs as a dictionary.
"""
return copy.copy(self.inputs)
def get_input_value_help(self,key):
if key == 'entryNumber': return 'An integer indicating the DABAM entry number or the remote profile files'
if key == 'silent': return 'Avoid printing information messages.'
if key == 'localFileRoot': return 'Define the name of local DABAM file root (<name>.dat for data, <name>.txt for metadata). If unset, use remote access'
if key == 'outputFileRoot': return 'Define the root for output files. Set to "" for no output. Default is "'+self.get_input_value("outputFileRoot")+'"'
if key == 'setDetrending': return 'Detrending: if >0 is the polynomial degree, -1=skip, -2=read from metadata DETRENDING, -3=ellipse(optimized), -4=ellipse(design). Default=%d'%self.get_input_value("setDetrending")
if key == 'detrendingWindowFactor': return 'detrendingWindowFactor: the fraction of the window used for fit (1.0 is full). Default=%f'%self.get_input_value("detrendingWindowFactor")
if key == 'resetZeroHeight': return 'resetZeroHeight: 0=None , 1=to minimum, 2=to center Default=%d'%self.get_input_value("resetZeroHeight")
if key == 'nbinS': return 'Number of bins for the slopes histogram in rads. Default is %d'%self.get_input_value("nbinS")
if key == 'nbinH': return 'Number of bins for the heights histogram in m. Default is %d'%self.get_input_value("nbinH")
if key == 'shadowCalc': return 'Write file with mesh for SHADOW. Default=No'
if key == 'shadowNy': return 'For SHADOW file, the number of points along Y (length). If negative, use the profile points. Default=%d'%self.get_input_value("shadowNy")
if key == 'shadowNx': return 'For SHADOW file, the number of points along X (width). Default=%d'%self.get_input_value("shadowNx")
if key == 'shadowWidth': return 'For SHADOW file, the surface dimension along X (width) in cm. Default=%4.2f'%self.get_input_value("shadowWidth")
if key == 'shadowFactor': return 'For SHADOW file, the factor from m to user units. Default=%4.2f'%self.get_input_value("shadowFactor")
if key == 'multiply': return 'Multiply input profile (slope or height) by this number (to play with StDev values). Default=%4.2f'%self.get_input_value("multiply")
if key == 'oversample': return 'Oversample factor for the number of abscissas points. 0=No oversample. (Default=%2.1f)'%self.get_input_value("oversample")
if key == 'useHeightsOrSlopes': return 'Force calculations using profile heights (0) or slopes (1). If -1, used metadata keyword FILE_FORMAT. Default=%d'%self.get_input_value("useHeightsOrSlopes")
if key == 'useAbscissasColumn': return 'Use abscissas column index. Default=%d use the metadata COLUMN_INDEX_ABSCISSAS or 0 if undefined'%self.get_input_value("useAbscissasColumn")
if key == 'useOrdinatesColumn': return 'Use ordinates column index. Default=%d use the metadata COLUMN_INDEX_ORDINATES or 1 if undefined'%self.get_input_value("useOrdinatesColumn")
if key == 'plot': return 'Plot: all heights slopes psd_h psd_s csd_h csd_s. histo_s histo_h acf_h acf_s. Default=%s'%repr(self.get_input_value("plot"))
if key == 'summary': return 'gets a summary of all DABAM profiles'
return ''
def get_input_value_short_name(self, key):
"""
Parameters
----------
key : str
The input key value.
Returns
-------
str
The short name (e.g. key='entryNumber', it returns 'N')
"""
if key == 'entryNumber': return 'N'
if key == 'silent': return 's'
if key == 'localFileRoot': return 'l'
if key == 'outputFileRoot': return 'r'
if key == 'setDetrending': return 'D'
if key == 'detrendingWindowFactor': return 'W'
if key == 'resetZeroHeight': return 'H'
if key == 'nbinS': return 'b'
if key == 'nbinH': return 'e'
if key == 'shadowCalc': return 'S'
if key == 'shadowNy': return 'y'
if key == 'shadowNx': return 'x'
if key == 'shadowWidth': return 'w'
if key == 'shadowFactor': return 'f'
if key == 'multiply': return 'm'
if key == 'oversample': return 'I'
if key == 'useHeightsOrSlopes': return 'Z'
if key == 'useAbscissasColumn': return 'A'
if key == 'useOrdinatesColumn': return 'O'
if key == 'plot': return 'P'
if key == 'summary': return 'Y'
return '?'
#
# file names
#
def file_metadata(self):
"""
Returns
-------
str
The name of the metadata file (with the extension .txt).
"""
return self._file_root()+'.txt'
def file_data(self):
"""
Returns
-------
str
The name of the data file (with the extension .dat).
"""
return self._file_root()+'.dat'
#
# load profile and store data. This is the main action!!
#
def load(self, entry=None):
"""
Parameters
----------
entry : int, optional
sets the current entry to this value before loading (default=None, using current set number).
"""
if entry is None:
pass
else:
self.set_input_entryNumber(entry)
# load data and metadata
self._load_file_metadata()
self._load_file_data()
# test consistency
if self.is_remote_access:
if self.get_input_value("entryNumber") <= 0:
raise Exception("Error: entry number must be non-zero positive for remote access.")
self.make_calculations()
def metadata_set_info(self,
YEAR_FABRICATION=None,
SURFACE_SHAPE=None,
FUNCTION=None,
LENGTH=None,
WIDTH=None,
THICK=None,
LENGTH_OPTICAL=None,
SUBSTRATE=None,
COATING=None,
FACILITY=None,
INSTRUMENT=None,
POLISHING=None,
ENVIRONMENT=None,
SCAN_DATE=None,
CALC_HEIGHT_RMS=None,
CALC_HEIGHT_RMS_FACTOR=None,
CALC_SLOPE_RMS=None,
CALC_SLOPE_RMS_FACTOR=None,
USER_EXAMPLE=None,
USER_REFERENCE=None,
USER_ADDED_BY=None,
):
"""
Sets the metadata info.
Parameters
----------
YEAR_FABRICATION :
the user value to be set.
SURFACE_SHAPE :
the user value to be set.
FUNCTION :
the user value to be set.
LENGTH :
the user value to be set.
WIDTH :
the user value to be set.
THICK :
the user value to be set.
LENGTH_OPTICAL :
the user value to be set.
SUBSTRATE :
the user value to be set.
COATING :
the user value to be set.
FACILITY :
the user value to be set.
INSTRUMENT :
the user value to be set.
POLISHING :
the user value to be set.
ENVIRONMENT :
the user value to be set.
SCAN_DATE :
the user value to be set.
CALC_HEIGHT_RMS :
the user value to be set.
CALC_HEIGHT_RMS_FACTOR :
the user value to be set.
CALC_SLOPE_RMS :
the user value to be set.
CALC_SLOPE_RMS_FACTOR :
the user value to be set.
USER_EXAMPLE :
the user value to be set.
USER_REFERENCE :
the user value to be set.
USER_ADDED_BY :
the user value to be set.
"""
#
# do not change these tags
#
# dm.metadata["FILE_FORMAT"] = None
# dm.metadata["FILE_HEADER_LINES"] = None
# dm.metadata["X1_FACTOR"] = None
# dm.metadata["COLUMN_INDEX_ORDINATES"] = None
# for i in range(4):
# dm.metadata["Y1_FACTOR"%(i+1)] = None
#
# for i in range(4):
# dm.metadata["PLOT_TITLE_X%d"%(i+1)] = None
# dm.metadata["PLOT_TITLE_Y%d"%(i+1)] = None
self.metadata["YEAR_FABRICATION"] = YEAR_FABRICATION
self.metadata["SURFACE_SHAPE"] = SURFACE_SHAPE
self.metadata["FUNCTION"] = FUNCTION
self.metadata["LENGTH"] = LENGTH
self.metadata["WIDTH"] = WIDTH
self.metadata["THICK"] = THICK
self.metadata["LENGTH_OPTICAL"] = LENGTH_OPTICAL
self.metadata["SUBSTRATE"] = SUBSTRATE
self.metadata["COATING"] = COATING
self.metadata["FACILITY"] = FACILITY
self.metadata["INSTRUMENT"] = INSTRUMENT
self.metadata["POLISHING"] = POLISHING
self.metadata["ENVIRONMENT"] = ENVIRONMENT
self.metadata["SCAN_DATE"] = SCAN_DATE
self.metadata["CALC_HEIGHT_RMS"] = CALC_HEIGHT_RMS
self.metadata["CALC_HEIGHT_RMS_FACTOR"] = CALC_HEIGHT_RMS_FACTOR
self.metadata["CALC_SLOPE_RMS"] = CALC_SLOPE_RMS
self.metadata["CALC_SLOPE_RMS_FACTOR"] = CALC_SLOPE_RMS_FACTOR
self.metadata["USER_EXAMPLE"] = USER_EXAMPLE
self.metadata["USER_REFERENCE"] = USER_REFERENCE
self.metadata["USER_ADDED_BY"] = USER_ADDED_BY
#
#calculations
#
def make_calculations(self):
"""
Once the inputs are set, use thos method to perform calculations (detrending, histograms, osd, etc.).
"""
#calculate detrended profiles
self._calc_detrended_profiles()
# reset heights
self._reset_heights()
#calculate psd
self._calc_psd()
#calculate histograms
self._calc_histograms()
#calculate moments
self.momentsHeights = moment(self.zHeights)
self.momentsSlopes = moment(self.zSlopes)
# write files
if self.get_input_value("outputFileRoot") != "":
self._write_output_files()
#write shadow file
if self.get_input_value("shadowCalc"):
self._write_file_for_shadow()
if not(self.get_input_value("silent")):
outFile = self.get_input_value("outputFileRoot")+'Shadow.dat'
print ("File "+outFile+" for SHADOW written to disk.")
#info
if not(self.get_input_value("silent")):
print(self.info_profiles())
def stdev_profile_heights(self):
"""
Gets the standard deviation of the heights profile
Returns
-------
float
"""
return self.zHeights.std(ddof=1)
def stdev_profile_slopes(self):
"""
Gets the standard deviation of the slopes profile
Returns
-------
float
"""
return self.zSlopes.std(ddof=1)
def stdev_psd_heights(self):
"""
Gets the standard deviation of the heights profile by integration of the PSD.
Returns
-------
float
"""
return numpy.sqrt(self.csdHeights[-1])
def stdev_psd_slopes(self):
"""
Gets the standard deviation of the slopes profile by integration of the PSD.
Returns
-------
float
"""
return numpy.sqrt(self.csdSlopes[-1])
def stdev_user_heights(self):
"""
Gets the standard deviation of the heights profile by retrieving the value stored in the metadata.
Returns
-------
float
"""
try:
if self.metadata['CALC_HEIGHT_RMS'] != None:
if self.metadata['CALC_HEIGHT_RMS_FACTOR'] != None:
return float(self.metadata['CALC_HEIGHT_RMS']) * float(self.metadata['CALC_HEIGHT_RMS_FACTOR'])
else:
return float(self.metadata['CALC_HEIGHT_RMS'])
except:
return None
def stdev_user_slopes(self):
"""
Gets the standard deviation of the slopes profile by retrieving the value stored in the metadata.
Returns
-------
float
"""
try:
if self.metadata['CALC_SLOPE_RMS'] != None:
if self.metadata['CALC_SLOPE_RMS_FACTOR'] != None:
return float(self.metadata['CALC_SLOPE_RMS']) * float(self.metadata['CALC_SLOPE_RMS_FACTOR'])
else:
return float(self.metadata['CALC_SLOPE_RMS'])
except: