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cgarciae/phi | phi/dsl.py | Expression.Seq | def Seq(self, *sequence, **kwargs):
"""
`Seq` is used to express function composition. The expression
Seq(f, g)
be equivalent to
lambda x: g(f(x))
As you see, its a little different from the mathematical definition. Excecution order flow from left to right, this makes reading and reasoning about cod... | python | def Seq(self, *sequence, **kwargs):
"""
`Seq` is used to express function composition. The expression
Seq(f, g)
be equivalent to
lambda x: g(f(x))
As you see, its a little different from the mathematical definition. Excecution order flow from left to right, this makes reading and reasoning about cod... | [
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cgarciae/phi | phi/dsl.py | Expression.With | def With(self, context_manager, *body, **kwargs):
"""
**With**
def With(context_manager, *body):
**Arguments**
* **context_manager**: a [context manager](https://docs.python.org/2/reference/datamodel.html#context-managers) object or valid expression from the DSL that returns a context manager.
* ***body*... | python | def With(self, context_manager, *body, **kwargs):
"""
**With**
def With(context_manager, *body):
**Arguments**
* **context_manager**: a [context manager](https://docs.python.org/2/reference/datamodel.html#context-managers) object or valid expression from the DSL that returns a context manager.
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cgarciae/phi | phi/dsl.py | Expression.ReadList | def ReadList(self, *branches, **kwargs):
"""
Same as `phi.dsl.Expression.List` but any string argument `x` is translated to `Read(x)`.
"""
branches = map(lambda x: E.Read(x) if isinstance(x, str) else x, branches)
return self.List(*branches, **kwargs) | python | def ReadList(self, *branches, **kwargs):
"""
Same as `phi.dsl.Expression.List` but any string argument `x` is translated to `Read(x)`.
"""
branches = map(lambda x: E.Read(x) if isinstance(x, str) else x, branches)
return self.List(*branches, **kwargs) | [
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cgarciae/phi | phi/dsl.py | Expression.Write | def Write(self, *state_args, **state_dict):
"""See `phi.dsl.Expression.Read`"""
if len(state_dict) + len(state_args) < 1:
raise Exception("Please include at-least 1 state variable, got {0} and {1}".format(state_args, state_dict))
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raise Exception("... | python | def Write(self, *state_args, **state_dict):
"""See `phi.dsl.Expression.Read`"""
if len(state_dict) + len(state_args) < 1:
raise Exception("Please include at-least 1 state variable, got {0} and {1}".format(state_args, state_dict))
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raise Exception("... | [
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cgarciae/phi | phi/dsl.py | Expression.Val | def Val(self, val, **kwargs):
"""
The expression
Val(a)
is equivalent to the constant function
lambda x: a
All expression in this module interprete values that are not functions as constant functions using `Val`, for example
Seq(1, P + 1)
is equivalent to
Seq(Val(1), P + 1)
The previous ... | python | def Val(self, val, **kwargs):
"""
The expression
Val(a)
is equivalent to the constant function
lambda x: a
All expression in this module interprete values that are not functions as constant functions using `Val`, for example
Seq(1, P + 1)
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cgarciae/phi | phi/dsl.py | Expression.If | def If(self, condition, *then, **kwargs):
"""
**If**
If(Predicate, *Then)
Having conditionals expressions a necesity in every language, Phi includes the `If` expression for such a purpose.
**Arguments**
* **Predicate** : a predicate expression uses to determine if the `Then` or `Else` branches should be... | python | def If(self, condition, *then, **kwargs):
"""
**If**
If(Predicate, *Then)
Having conditionals expressions a necesity in every language, Phi includes the `If` expression for such a purpose.
**Arguments**
* **Predicate** : a predicate expression uses to determine if the `Then` or `Else` branches should be... | [
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cgarciae/phi | phi/dsl.py | Expression.Else | def Else(self, *Else, **kwargs):
"""See `phi.dsl.Expression.If`"""
root = self._root
ast = self._ast
next_else = E.Seq(*Else)._f
ast = _add_else(ast, next_else)
g = _compile_if(ast)
return root.__then__(g, **kwargs) | python | def Else(self, *Else, **kwargs):
"""See `phi.dsl.Expression.If`"""
root = self._root
ast = self._ast
next_else = E.Seq(*Else)._f
ast = _add_else(ast, next_else)
g = _compile_if(ast)
return root.__then__(g, **kwargs) | [
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alvinlindstam/grapheme | grapheme/api.py | length | def length(string, until=None):
"""
Returns the number of graphemes in the string.
Note that this functions needs to traverse the full string to calculate the length,
unlike `len(string)` and it's time consumption is linear to the length of the string
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Only counts up ... | python | def length(string, until=None):
"""
Returns the number of graphemes in the string.
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alvinlindstam/grapheme | grapheme/api.py | slice | def slice(string, start=None, end=None):
"""
Returns a substring of the given string, counting graphemes instead of codepoints.
Negative indices is currently not supported.
>>> string = "tamil நி (ni)"
>>> string[:7]
'tamil ந'
>>> grapheme.slice(string, end=7)
'tamil நி'
>>> string... | python | def slice(string, start=None, end=None):
"""
Returns a substring of the given string, counting graphemes instead of codepoints.
Negative indices is currently not supported.
>>> string = "tamil நி (ni)"
>>> string[:7]
'tamil ந'
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'tamil நி'
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alvinlindstam/grapheme | grapheme/api.py | contains | def contains(string, substring):
"""
Returns true if the sequence of graphemes in substring is also present in string.
This differs from the normal python `in` operator, since the python operator will return
true if the sequence of codepoints are withing the other string without considering
graphem... | python | def contains(string, substring):
"""
Returns true if the sequence of graphemes in substring is also present in string.
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alvinlindstam/grapheme | grapheme/api.py | startswith | def startswith(string, prefix):
"""
Like str.startswith, but also checks that the string starts with the given prefixes sequence of graphemes.
str.startswith may return true for a prefix that is not visually represented as a prefix if a grapheme cluster
is continued after the prefix ends.
>>> grap... | python | def startswith(string, prefix):
"""
Like str.startswith, but also checks that the string starts with the given prefixes sequence of graphemes.
str.startswith may return true for a prefix that is not visually represented as a prefix if a grapheme cluster
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>>> grapheme.startswith("✊🏾", "✊")
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alvinlindstam/grapheme | grapheme/api.py | endswith | def endswith(string, suffix):
"""
Like str.endswith, but also checks that the string ends with the given prefixes sequence of graphemes.
str.endswith may return true for a suffix that is not visually represented as a suffix if a grapheme cluster
is initiated before the suffix starts.
>>> grapheme.... | python | def endswith(string, suffix):
"""
Like str.endswith, but also checks that the string ends with the given prefixes sequence of graphemes.
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alvinlindstam/grapheme | grapheme/api.py | safe_split_index | def safe_split_index(string, max_len):
"""
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"""
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awacha/sastool | sastool/io/header.py | readB1logfile | def readB1logfile(filename):
"""Read B1 logfile (*.log)
Inputs:
filename: the file name
Output: A dictionary.
"""
dic = dict()
# try to open. If this fails, an exception is raised
with open(filename, 'rt', encoding='utf-8') as f:
for l in f:
l = l.strip()
... | python | def readB1logfile(filename):
"""Read B1 logfile (*.log)
Inputs:
filename: the file name
Output: A dictionary.
"""
dic = dict()
# try to open. If this fails, an exception is raised
with open(filename, 'rt', encoding='utf-8') as f:
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awacha/sastool | sastool/io/header.py | writeB1logfile | def writeB1logfile(filename, data):
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filename: name of the file.
data: header dictionary
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filename: name of the file.
data: header dictionary
Notes:
exceptions pass through to the caller.
"""
allkeys = list(data.keys())
f = open(filename, 'wt', encoding='utf-8')
fo... | [
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awacha/sastool | sastool/io/header.py | readB1header | def readB1header(filename):
"""Read beamline B1 (HASYLAB, Hamburg) header data
Input
-----
filename: string
the file name. If ends with ``.gz``, it is fed through a ``gunzip``
filter
Output
------
A header dictionary.
Examples
--------
read header data from 'OR... | python | def readB1header(filename):
"""Read beamline B1 (HASYLAB, Hamburg) header data
Input
-----
filename: string
the file name. If ends with ``.gz``, it is fed through a ``gunzip``
filter
Output
------
A header dictionary.
Examples
--------
read header data from 'OR... | [
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read header data from 'ORG000123.DAT'::
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awacha/sastool | sastool/io/header.py | _readedf_extractline | def _readedf_extractline(left, right):
"""Helper function to interpret lines in an EDF file header.
"""
functions = [int, float, lambda l:float(l.split(None, 1)[0]),
lambda l:int(l.split(None, 1)[0]),
dateutil.parser.parse, lambda x:str(x)]
for f in functions:
t... | python | def _readedf_extractline(left, right):
"""Helper function to interpret lines in an EDF file header.
"""
functions = [int, float, lambda l:float(l.split(None, 1)[0]),
lambda l:int(l.split(None, 1)[0]),
dateutil.parser.parse, lambda x:str(x)]
for f in functions:
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awacha/sastool | sastool/io/header.py | readehf | def readehf(filename):
"""Read EDF header (ESRF data format, as of beamline ID01 and ID02)
Input
-----
filename: string
the file name to load
Output
------
the EDF header structure in a dictionary
"""
f = open(filename, 'r')
edf = {}
if not f.readline().strip().star... | python | def readehf(filename):
"""Read EDF header (ESRF data format, as of beamline ID01 and ID02)
Input
-----
filename: string
the file name to load
Output
------
the EDF header structure in a dictionary
"""
f = open(filename, 'r')
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awacha/sastool | sastool/io/header.py | readbhfv1 | def readbhfv1(filename, load_data=False, bdfext='.bdf', bhfext='.bhf'):
"""Read header data from bdf/bhf file (Bessy Data Format v1)
Input:
filename: the name of the file
load_data: if the matrices are to be loaded
Output:
bdf: the BDF header structure
Adapted the bdf_read.m m... | python | def readbhfv1(filename, load_data=False, bdfext='.bdf', bhfext='.bhf'):
"""Read header data from bdf/bhf file (Bessy Data Format v1)
Input:
filename: the name of the file
load_data: if the matrices are to be loaded
Output:
bdf: the BDF header structure
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awacha/sastool | sastool/io/header.py | readmarheader | def readmarheader(filename):
"""Read a header from a MarResearch .image file."""
with open(filename, 'rb') as f:
intheader = np.fromstring(f.read(10 * 4), np.int32)
floatheader = np.fromstring(f.read(15 * 4), '<f4')
strheader = f.read(24)
f.read(4)
otherstrings = [f.read(... | python | def readmarheader(filename):
"""Read a header from a MarResearch .image file."""
with open(filename, 'rb') as f:
intheader = np.fromstring(f.read(10 * 4), np.int32)
floatheader = np.fromstring(f.read(15 * 4), '<f4')
strheader = f.read(24)
f.read(4)
otherstrings = [f.read(... | [
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awacha/sastool | sastool/io/header.py | readBerSANS | def readBerSANS(filename):
"""Read a header from a SANS file (produced usually by BerSANS)"""
hed = {'Comment': ''}
translate = {'Lambda': 'Wavelength',
'Title': 'Owner',
'SampleName': 'Title',
'BeamcenterX': 'BeamPosY',
'BeamcenterY': 'Bea... | python | def readBerSANS(filename):
"""Read a header from a SANS file (produced usually by BerSANS)"""
hed = {'Comment': ''}
translate = {'Lambda': 'Wavelength',
'Title': 'Owner',
'SampleName': 'Title',
'BeamcenterX': 'BeamPosY',
'BeamcenterY': 'Bea... | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Sine | def Sine(x, a, omega, phi, y0):
"""Sine function
Inputs:
-------
``x``: independent variable
``a``: amplitude
``omega``: circular frequency
``phi``: phase
``y0``: offset
Formula:
--------
``a*sin(x*omega + phi)+y0``
"""
return a * np.sin(x * ... | python | def Sine(x, a, omega, phi, y0):
"""Sine function
Inputs:
-------
``x``: independent variable
``a``: amplitude
``omega``: circular frequency
``phi``: phase
``y0``: offset
Formula:
--------
``a*sin(x*omega + phi)+y0``
"""
return a * np.sin(x * ... | [
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``x``: independent variable
``a``: amplitude
``omega``: circular frequency
``phi``: phase
``y0``: offset
Formula:
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``a*sin(x*omega + phi)+y0`` | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Cosine | def Cosine(x, a, omega, phi, y0):
"""Cosine function
Inputs:
-------
``x``: independent variable
``a``: amplitude
``omega``: circular frequency
``phi``: phase
``y0``: offset
Formula:
--------
``a*cos(x*omega + phi)+y0``
"""
return a * np.cos(... | python | def Cosine(x, a, omega, phi, y0):
"""Cosine function
Inputs:
-------
``x``: independent variable
``a``: amplitude
``omega``: circular frequency
``phi``: phase
``y0``: offset
Formula:
--------
``a*cos(x*omega + phi)+y0``
"""
return a * np.cos(... | [
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Inputs:
-------
``x``: independent variable
``a``: amplitude
``omega``: circular frequency
``phi``: phase
``y0``: offset
Formula:
--------
``a*cos(x*omega + phi)+y0`` | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Square | def Square(x, a, b, c):
"""Second order polynomial
Inputs:
-------
``x``: independent variable
``a``: coefficient of the second-order term
``b``: coefficient of the first-order term
``c``: additive constant
Formula:
--------
``a*x^2 + b*x + c``
"""
r... | python | def Square(x, a, b, c):
"""Second order polynomial
Inputs:
-------
``x``: independent variable
``a``: coefficient of the second-order term
``b``: coefficient of the first-order term
``c``: additive constant
Formula:
--------
``a*x^2 + b*x + c``
"""
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Inputs:
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``x``: independent variable
``a``: coefficient of the second-order term
``b``: coefficient of the first-order term
``c``: additive constant
Formula:
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``a*x^2 + b*x + c`` | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Cube | def Cube(x, a, b, c, d):
"""Third order polynomial
Inputs:
-------
``x``: independent variable
``a``: coefficient of the third-order term
``b``: coefficient of the second-order term
``c``: coefficient of the first-order term
``d``: additive constant
Formula:
... | python | def Cube(x, a, b, c, d):
"""Third order polynomial
Inputs:
-------
``x``: independent variable
``a``: coefficient of the third-order term
``b``: coefficient of the second-order term
``c``: coefficient of the first-order term
``d``: additive constant
Formula:
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``x``: independent variable
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``c``: coefficient of the first-order term
``d``: additive constant
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``a*x^3 + b*x^... | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Exponential | def Exponential(x, a, tau, y0):
"""Exponential function
Inputs:
-------
``x``: independent variable
``a``: scaling factor
``tau``: time constant
``y0``: additive constant
Formula:
--------
``a*exp(x/tau)+y0``
"""
return np.exp(x / tau) * a + y0 | python | def Exponential(x, a, tau, y0):
"""Exponential function
Inputs:
-------
``x``: independent variable
``a``: scaling factor
``tau``: time constant
``y0``: additive constant
Formula:
--------
``a*exp(x/tau)+y0``
"""
return np.exp(x / tau) * a + y0 | [
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``x``: independent variable
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``y0``: additive constant
Formula:
--------
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Lorentzian | def Lorentzian(x, a, x0, sigma, y0):
"""Lorentzian peak
Inputs:
-------
``x``: independent variable
``a``: scaling factor (extremal value)
``x0``: center
``sigma``: half width at half maximum
``y0``: additive constant
Formula:
--------
``a/(1+((x-x0)... | python | def Lorentzian(x, a, x0, sigma, y0):
"""Lorentzian peak
Inputs:
-------
``x``: independent variable
``a``: scaling factor (extremal value)
``x0``: center
``sigma``: half width at half maximum
``y0``: additive constant
Formula:
--------
``a/(1+((x-x0)... | [
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``a/(1+((x-x0)/sigma)^2)+y0`` | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | Gaussian | def Gaussian(x, a, x0, sigma, y0):
"""Gaussian peak
Inputs:
-------
``x``: independent variable
``a``: scaling factor (extremal value)
``x0``: center
``sigma``: half width at half maximum
``y0``: additive constant
Formula:
--------
``a*exp(-(x-x0)^2)... | python | def Gaussian(x, a, x0, sigma, y0):
"""Gaussian peak
Inputs:
-------
``x``: independent variable
``a``: scaling factor (extremal value)
``x0``: center
``sigma``: half width at half maximum
``y0``: additive constant
Formula:
--------
``a*exp(-(x-x0)^2)... | [
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awacha/sastool | sastool/fitting/fitfunctions/basic.py | LogNormal | def LogNormal(x, a, mu, sigma):
"""PDF of a log-normal distribution
Inputs:
-------
``x``: independent variable
``a``: amplitude
``mu``: center parameter
``sigma``: width parameter
Formula:
--------
``a/ (2*pi*sigma^2*x^2)^0.5 * exp(-(log(x)-mu)^2/(2*sigma^2... | python | def LogNormal(x, a, mu, sigma):
"""PDF of a log-normal distribution
Inputs:
-------
``x``: independent variable
``a``: amplitude
``mu``: center parameter
``sigma``: width parameter
Formula:
--------
``a/ (2*pi*sigma^2*x^2)^0.5 * exp(-(log(x)-mu)^2/(2*sigma^2... | [
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``a/ (2*pi*sigma^2*x^2)^0.5 * exp(-(log(x)-mu)^2/(2*sigma^2)) | [
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awacha/sastool | sastool/utils2d/integrate.py | radintpix | def radintpix(data, dataerr, bcx, bcy, mask=None, pix=None, returnavgpix=False,
phi0=0, dphi=0, returnmask=False, symmetric_sector=False,
doslice=False, errorpropagation=2, autoqrange_linear=True):
"""Radial integration (averaging) on the detector plane
Inputs:
data: scatter... | python | def radintpix(data, dataerr, bcx, bcy, mask=None, pix=None, returnavgpix=False,
phi0=0, dphi=0, returnmask=False, symmetric_sector=False,
doslice=False, errorpropagation=2, autoqrange_linear=True):
"""Radial integration (averaging) on the detector plane
Inputs:
data: scatter... | [
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awacha/sastool | sastool/utils2d/integrate.py | azimintpix | def azimintpix(data, dataerr, bcx, bcy, mask=None, Ntheta=100, pixmin=0,
pixmax=np.inf, returnmask=False, errorpropagation=2):
"""Azimuthal integration (averaging) on the detector plane
Inputs:
data: scattering pattern matrix (np.ndarray, dtype: np.double)
dataerr: error matrix (... | python | def azimintpix(data, dataerr, bcx, bcy, mask=None, Ntheta=100, pixmin=0,
pixmax=np.inf, returnmask=False, errorpropagation=2):
"""Azimuthal integration (averaging) on the detector plane
Inputs:
data: scattering pattern matrix (np.ndarray, dtype: np.double)
dataerr: error matrix (... | [
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awacha/sastool | sastool/misc/searchpath.py | find_subdirs | def find_subdirs(startdir='.', recursion_depth=None):
"""Find all subdirectory of a directory.
Inputs:
startdir: directory to start with. Defaults to the current folder.
recursion_depth: number of levels to traverse. None is infinite.
Output: a list of absolute names of subfolders.
Ex... | python | def find_subdirs(startdir='.', recursion_depth=None):
"""Find all subdirectory of a directory.
Inputs:
startdir: directory to start with. Defaults to the current folder.
recursion_depth: number of levels to traverse. None is infinite.
Output: a list of absolute names of subfolders.
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awacha/sastool | sastool/misc/basicfit.py | findpeak | def findpeak(x, y, dy=None, position=None, hwhm=None, baseline=None, amplitude=None, curve='Lorentz'):
"""Find a (positive) peak in the dataset.
This function is deprecated, please consider using findpeak_single() instead.
Inputs:
x, y, dy: abscissa, ordinate and the error of the ordinate (can... | python | def findpeak(x, y, dy=None, position=None, hwhm=None, baseline=None, amplitude=None, curve='Lorentz'):
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This function is deprecated, please consider using findpeak_single() instead.
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awacha/sastool | sastool/misc/basicfit.py | findpeak_single | def findpeak_single(x, y, dy=None, position=None, hwhm=None, baseline=None, amplitude=None, curve='Lorentz',
return_stat=False, signs=(-1, 1), return_x=None):
"""Find a (positive or negative) peak in the dataset.
Inputs:
x, y, dy: abscissa, ordinate and the error of the ordinate (ca... | python | def findpeak_single(x, y, dy=None, position=None, hwhm=None, baseline=None, amplitude=None, curve='Lorentz',
return_stat=False, signs=(-1, 1), return_x=None):
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awacha/sastool | sastool/misc/basicfit.py | findpeak_multi | def findpeak_multi(x, y, dy, N, Ntolerance, Nfit=None, curve='Lorentz', return_xfit=False, return_stat=False):
"""Find multiple peaks in the dataset given by vectors x and y.
Points are searched for in the dataset where the N points before and
after have strictly lower values than them. To get rid of false... | python | def findpeak_multi(x, y, dy, N, Ntolerance, Nfit=None, curve='Lorentz', return_xfit=False, return_stat=False):
"""Find multiple peaks in the dataset given by vectors x and y.
Points are searched for in the dataset where the N points before and
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awacha/sastool | sastool/misc/basicfit.py | findpeak_asymmetric | def findpeak_asymmetric(x, y, dy=None, curve='Lorentz', return_x=None, init_parameters=None):
"""Find an asymmetric Lorentzian peak.
Inputs:
x: numpy array of the abscissa
y: numpy array of the ordinate
dy: numpy array of the errors in y (or None if not present)
curve: string (c... | python | def findpeak_asymmetric(x, y, dy=None, curve='Lorentz', return_x=None, init_parameters=None):
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Inputs:
x: numpy array of the abscissa
y: numpy array of the ordinate
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awacha/sastool | sastool/io/onedim.py | readspecscan | def readspecscan(f, number=None):
"""Read the next spec scan in the file, which starts at the current position."""
scan = None
scannumber = None
while True:
l = f.readline()
if l.startswith('#S'):
scannumber = int(l[2:].split()[0])
if not ((number is None) or (num... | python | def readspecscan(f, number=None):
"""Read the next spec scan in the file, which starts at the current position."""
scan = None
scannumber = None
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l = f.readline()
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awacha/sastool | sastool/io/onedim.py | readspec | def readspec(filename, read_scan=None):
"""Open a SPEC file and read its content
Inputs:
filename: string
the file to open
read_scan: None, 'all' or integer
the index of scan to be read from the file. If None, no scan should be read. If
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filename: string
the file to open
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awacha/sastool | sastool/io/onedim.py | readabt | def readabt(filename, dirs='.'):
"""Read abt_*.fio type files from beamline B1, HASYLAB.
Input:
filename: the name of the file.
dirs: directories to search for files in
Output:
A dictionary. The fields are self-explanatory.
"""
# resolve filename
filename = misc.findfil... | python | def readabt(filename, dirs='.'):
"""Read abt_*.fio type files from beamline B1, HASYLAB.
Input:
filename: the name of the file.
dirs: directories to search for files in
Output:
A dictionary. The fields are self-explanatory.
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awacha/sastool | sastool/io/credo_cpth5/header.py | Header.energy | def energy(self) -> ErrorValue:
"""X-ray energy"""
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sel... | python | def energy(self) -> ErrorValue:
"""X-ray energy"""
return (ErrorValue(*(scipy.constants.physical_constants['speed of light in vacuum'][0::2])) *
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awacha/sastool | sastool/io/credo_cpth5/header.py | Header.maskname | def maskname(self) -> Optional[str]:
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awacha/sastool | sastool/utils2d/centering.py | findbeam_gravity | def findbeam_gravity(data, mask):
"""Find beam center with the "gravity" method
Inputs:
data: scattering image
mask: mask matrix
Output:
a vector of length 2 with the x (row) and y (column) coordinates
of the origin, starting from 1
"""
# for each row and column fi... | python | def findbeam_gravity(data, mask):
"""Find beam center with the "gravity" method
Inputs:
data: scattering image
mask: mask matrix
Output:
a vector of length 2 with the x (row) and y (column) coordinates
of the origin, starting from 1
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awacha/sastool | sastool/utils2d/centering.py | findbeam_slices | def findbeam_slices(data, orig_initial, mask=None, maxiter=0, epsfcn=0.001,
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Inputs:
data: scattering matrix
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awacha/sastool | sastool/utils2d/centering.py | findbeam_azimuthal | def findbeam_azimuthal(data, orig_initial, mask=None, maxiter=100, Ntheta=50,
dmin=0, dmax=np.inf, extent=10, callback=None):
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Inputs:
data: scattering matrix
orig_initial: estimated value for x (row) and y (column)
... | python | def findbeam_azimuthal(data, orig_initial, mask=None, maxiter=100, Ntheta=50,
dmin=0, dmax=np.inf, extent=10, callback=None):
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data: scattering matrix
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awacha/sastool | sastool/utils2d/centering.py | findbeam_azimuthal_fold | def findbeam_azimuthal_fold(data, orig_initial, mask=None, maxiter=100,
Ntheta=50, dmin=0, dmax=np.inf, extent=10, callback=None):
"""Find beam center using azimuthal integration and folding
Inputs:
data: scattering matrix
orig_initial: estimated value for x (row) an... | python | def findbeam_azimuthal_fold(data, orig_initial, mask=None, maxiter=100,
Ntheta=50, dmin=0, dmax=np.inf, extent=10, callback=None):
"""Find beam center using azimuthal integration and folding
Inputs:
data: scattering matrix
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awacha/sastool | sastool/utils2d/centering.py | findbeam_semitransparent | def findbeam_semitransparent(data, pri, threshold=0.05):
"""Find beam with 2D weighting of semitransparent beamstop area
Inputs:
data: scattering matrix
pri: list of four: [xmin,xmax,ymin,ymax] for the borders of the beam
area under the semitransparent beamstop. X corresponds to the... | python | def findbeam_semitransparent(data, pri, threshold=0.05):
"""Find beam with 2D weighting of semitransparent beamstop area
Inputs:
data: scattering matrix
pri: list of four: [xmin,xmax,ymin,ymax] for the borders of the beam
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awacha/sastool | sastool/utils2d/centering.py | findbeam_radialpeak | def findbeam_radialpeak(data, orig_initial, mask, rmin, rmax, maxiter=100,
drive_by='amplitude', extent=10, callback=None):
"""Find the beam by minimizing the width of a peak in the radial average.
Inputs:
data: scattering matrix
orig_initial: first guess for the origin
... | python | def findbeam_radialpeak(data, orig_initial, mask, rmin, rmax, maxiter=100,
drive_by='amplitude', extent=10, callback=None):
"""Find the beam by minimizing the width of a peak in the radial average.
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data: scattering matrix
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... | [
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awacha/sastool | sastool/utils2d/centering.py | findbeam_Guinier | def findbeam_Guinier(data, orig_initial, mask, rmin, rmax, maxiter=100,
extent=10, callback=None):
"""Find the beam by minimizing the width of a Gaussian centered at the
origin (i.e. maximizing the radius of gyration in a Guinier scattering).
Inputs:
data: scattering matrix
... | python | def findbeam_Guinier(data, orig_initial, mask, rmin, rmax, maxiter=100,
extent=10, callback=None):
"""Find the beam by minimizing the width of a Gaussian centered at the
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data: scattering matrix
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awacha/sastool | sastool/utils2d/centering.py | findbeam_powerlaw | def findbeam_powerlaw(data, orig_initial, mask, rmin, rmax, maxiter=100,
drive_by='R2', extent=10, callback=None):
"""Find the beam by minimizing the width of a Gaussian centered at the
origin (i.e. maximizing the radius of gyration in a Guinier scattering).
Inputs:
data: scat... | python | def findbeam_powerlaw(data, orig_initial, mask, rmin, rmax, maxiter=100,
drive_by='R2', extent=10, callback=None):
"""Find the beam by minimizing the width of a Gaussian centered at the
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awacha/sastool | sastool/io/credo_cct/header.py | Header.beamcenterx | def beamcenterx(self) -> ErrorValue:
"""X (column) coordinate of the beam center, pixel units, 0-based."""
try:
return ErrorValue(self._data['geometry']['beamposy'],
self._data['geometry']['beamposy.err'])
except KeyError:
return ErrorValue(s... | python | def beamcenterx(self) -> ErrorValue:
"""X (column) coordinate of the beam center, pixel units, 0-based."""
try:
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awacha/sastool | sastool/io/credo_cct/header.py | Header.beamcentery | def beamcentery(self) -> ErrorValue:
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awacha/sastool | sastool/io/credo_cct/header.py | Header.maskname | def maskname(self) -> Optional[str]:
"""Name of the mask matrix file."""
mask = self._data['geometry']['mask']
if os.path.abspath(mask):
mask = os.path.split(mask)[-1]
return mask | python | def maskname(self) -> Optional[str]:
"""Name of the mask matrix file."""
mask = self._data['geometry']['mask']
if os.path.abspath(mask):
mask = os.path.split(mask)[-1]
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awacha/sastool | sastool/classes2/curve.py | errtrapz | def errtrapz(x, yerr):
"""Error of the trapezoid formula
Inputs:
x: the abscissa
yerr: the error of the dependent variable
Outputs:
the error of the integral
"""
x = np.array(x)
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yerr = np.array(yerr)
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"""Error of the trapezoid formula
Inputs:
x: the abscissa
yerr: the error of the dependent variable
Outputs:
the error of the integral
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awacha/sastool | sastool/classes2/curve.py | Curve.fit | def fit(self, fitfunction, parinit, unfittableparameters=(), *args, **kwargs):
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... | python | def fit(self, fitfunction, parinit, unfittableparameters=(), *args, **kwargs):
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awacha/sastool | sastool/classes2/curve.py | Curve.momentum | def momentum(self, exponent=1, errorrequested=True):
"""Calculate momenta (integral of y times x^exponent)
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Inputs:
exponent: the exponent of q in the integration.
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"""Calculate momenta (integral of y times x^exponent)
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awacha/sastool | sastool/classes2/curve.py | Curve.scalefactor | def scalefactor(self, other, qmin=None, qmax=None, Npoints=None):
"""Calculate a scaling factor, by which this curve is to be multiplied to best fit the other one.
Inputs:
other: the other curve (an instance of GeneralCurve or of a subclass of it)
qmin: lower cut-off (None to de... | python | def scalefactor(self, other, qmin=None, qmax=None, Npoints=None):
"""Calculate a scaling factor, by which this curve is to be multiplied to best fit the other one.
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other: the other curve (an instance of GeneralCurve or of a subclass of it)
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awacha/sastool | sastool/misc/fitter.py | Fitter._substitute_fixed_parameters_covar | def _substitute_fixed_parameters_covar(self, covar):
"""Insert fixed parameters in a covariance matrix"""
covar_resolved = np.empty((len(self._fixed_parameters), len(self._fixed_parameters)))
indices_of_fixed_parameters = [i for i in range(len(self.parameters())) if
... | python | def _substitute_fixed_parameters_covar(self, covar):
"""Insert fixed parameters in a covariance matrix"""
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awacha/sastool | sastool/io/credo_cct/loader.py | Loader.loadmask | def loadmask(self, filename: str) -> np.ndarray:
"""Load a mask file."""
mask = scipy.io.loadmat(self.find_file(filename, what='mask'))
maskkey = [k for k in mask.keys() if not (k.startswith('_') or k.endswith('_'))][0]
return mask[maskkey].astype(np.bool) | python | def loadmask(self, filename: str) -> np.ndarray:
"""Load a mask file."""
mask = scipy.io.loadmat(self.find_file(filename, what='mask'))
maskkey = [k for k in mask.keys() if not (k.startswith('_') or k.endswith('_'))][0]
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awacha/sastool | sastool/io/credo_cct/loader.py | Loader.loadcurve | def loadcurve(self, fsn: int) -> classes2.Curve:
"""Load a radial scattering curve"""
return classes2.Curve.new_from_file(self.find_file(self._exposureclass + '_%05d.txt' % fsn)) | python | def loadcurve(self, fsn: int) -> classes2.Curve:
"""Load a radial scattering curve"""
return classes2.Curve.new_from_file(self.find_file(self._exposureclass + '_%05d.txt' % fsn)) | [
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awacha/sastool | sastool/io/twodim.py | readcbf | def readcbf(name, load_header=False, load_data=True, for_nexus=False):
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load_data: bool
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"""Read a cbf (crystallographic binary format) file from a Dectris PILATUS
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awacha/sastool | sastool/io/twodim.py | readbdfv1 | def readbdfv1(filename, bdfext='.bdf', bhfext='.bhf'):
"""Read bdf file (Bessy Data Format v1)
Input
-----
filename: string
the name of the file
Output
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the BDF structure in a dict
Notes
-----
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... | python | def readbdfv1(filename, bdfext='.bdf', bhfext='.bhf'):
"""Read bdf file (Bessy Data Format v1)
Input
-----
filename: string
the name of the file
Output
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the BDF structure in a dict
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awacha/sastool | sastool/io/twodim.py | readint2dnorm | def readint2dnorm(filename):
"""Read corrected intensity and error matrices (Matlab mat or numpy npz
format for Beamline B1 (HASYLAB/DORISIII))
Input
-----
filename: string
the name of the file
Outputs
-------
two ``np.ndarray``-s, the Intensity and the Error matrices
File... | python | def readint2dnorm(filename):
"""Read corrected intensity and error matrices (Matlab mat or numpy npz
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Input
-----
filename: string
the name of the file
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awacha/sastool | sastool/io/twodim.py | writeint2dnorm | def writeint2dnorm(filename, Intensity, Error=None):
"""Save the intensity and error matrices to a file
Inputs
------
filename: string
the name of the file
Intensity: np.ndarray
the intensity matrix
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filename: string
the name of the file
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the intensity matrix
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awacha/sastool | sastool/io/twodim.py | readmask | def readmask(filename, fieldname=None):
"""Try to load a maskfile from a matlab(R) matrix file
Inputs
------
filename: string
the input file name
fieldname: string, optional
field in the mat file. None to autodetect.
Outputs
-------
the mask in a numpy array of type np.... | python | def readmask(filename, fieldname=None):
"""Try to load a maskfile from a matlab(R) matrix file
Inputs
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filename: string
the input file name
fieldname: string, optional
field in the mat file. None to autodetect.
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awacha/sastool | sastool/io/twodim.py | readedf | def readedf(filename):
"""Read an ESRF data file (measured at beamlines ID01 or ID02)
Inputs
------
filename: string
the input file name
Output
------
the imported EDF structure in a dict. The scattering pattern is under key
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Notes
-----
Only datatype ``Floa... | python | def readedf(filename):
"""Read an ESRF data file (measured at beamlines ID01 or ID02)
Inputs
------
filename: string
the input file name
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the imported EDF structure in a dict. The scattering pattern is under key
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awacha/sastool | sastool/io/twodim.py | readbdfv2 | def readbdfv2(filename, bdfext='.bdf', bhfext='.bhf'):
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Inputs
------
filename: string
the name of the input file. One can give the complete header or datafile
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bdfext: string, optional
the ... | python | def readbdfv2(filename, bdfext='.bdf', bhfext='.bhf'):
"""Read a version 2 Bessy Data File
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filename: string
the name of the input file. One can give the complete header or datafile
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bdfext: string, optional
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awacha/sastool | sastool/io/twodim.py | readmar | def readmar(filename):
"""Read a two-dimensional scattering pattern from a MarResearch .image file.
"""
hed = header.readmarheader(filename)
with open(filename, 'rb') as f:
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"""Read a two-dimensional scattering pattern from a MarResearch .image file.
"""
hed = header.readmarheader(filename)
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h = f.read(hed['recordlength'])
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awacha/sastool | sastool/io/twodim.py | writebdfv2 | def writebdfv2(filename, bdf, bdfext='.bdf', bhfext='.bhf'):
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Inputs
------
filename: string
the name of the output file. One can give the complete header or
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bdf: dict
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filename: string
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awacha/sastool | sastool/io/twodim.py | rebinmask | def rebinmask(mask, binx, biny, enlarge=False):
"""Re-bin (shrink or enlarge) a mask matrix.
Inputs
------
mask: np.ndarray
mask matrix.
binx: integer
binning along the 0th axis
biny: integer
binning along the 1st axis
enlarge: bool, optional
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"""Re-bin (shrink or enlarge) a mask matrix.
Inputs
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mask: np.ndarray
mask matrix.
binx: integer
binning along the 0th axis
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ClearcodeHQ/querystringsafe_base64 | src/querystringsafe_base64/__init__.py | fill_padding | def fill_padding(padded_string):
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Fill up missing padding in a string.
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:param str padded_string: string to be decoded that might miss pa... | python | def fill_padding(padded_string):
# type: (bytes) -> bytes
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Fill up missing padding in a string.
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ClearcodeHQ/querystringsafe_base64 | src/querystringsafe_base64/__init__.py | decode | def decode(encoded):
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Decode the result of querystringsafe_base64_encode or a regular base64.
.. note ::
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awacha/sastool | sastool/misc/utils.py | normalize_listargument | def normalize_listargument(arg):
"""Check if arg is an iterable (list, tuple, set, dict, np.ndarray, except
string!). If not, make a list of it. Numpy arrays are flattened and
converted to lists."""
if isinstance(arg, np.ndarray):
return arg.flatten()
if isinstance(arg, str):
... | python | def normalize_listargument(arg):
"""Check if arg is an iterable (list, tuple, set, dict, np.ndarray, except
string!). If not, make a list of it. Numpy arrays are flattened and
converted to lists."""
if isinstance(arg, np.ndarray):
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awacha/sastool | sastool/misc/utils.py | parse_number | def parse_number(val, use_dateutilparser=False):
"""Try to auto-detect the numeric type of the value. First a conversion to
int is tried. If this fails float is tried, and if that fails too, unicode()
is executed. If this also fails, a ValueError is raised.
"""
if use_dateutilparser:
funcs =... | python | def parse_number(val, use_dateutilparser=False):
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awacha/sastool | sastool/misc/utils.py | flatten_hierarchical_dict | def flatten_hierarchical_dict(original_dict, separator='.', max_recursion_depth=None):
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the dictionary to flatten
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the separator item in the keys of the flattened dictionary
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the dictionary to flatten
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the separator item in the keys of the flattened dictionary
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awacha/sastool | sastool/misc/utils.py | random_str | def random_str(Nchars=6, randstrbase='0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'):
"""Return a random string of <Nchars> characters. Characters are sampled
uniformly from <randstrbase>.
"""
return ''.join([randstrbase[random.randint(0, len(randstrbase) - 1)] for i in range(Nchars)]) | python | def random_str(Nchars=6, randstrbase='0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'):
"""Return a random string of <Nchars> characters. Characters are sampled
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awacha/sastool | sastool/io/statistics.py | listB1 | def listB1(fsns, xlsname, dirs, whattolist = None, headerformat = 'org_%05d.header'):
""" getsamplenames revisited, XLS output.
Inputs:
fsns: FSN sequence
xlsname: XLS file name to output listing
dirs: either a single directory (string) or a list of directories, a la readheader()
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""" getsamplenames revisited, XLS output.
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fsns: FSN sequence
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awacha/sastool | sastool/fitting/standalone.py | fit_shullroess | def fit_shullroess(q, Intensity, Error, R0=None, r=None):
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vector of the q values (4*pi*sin(theta)/lambda)
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Intensity vector
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q: np.ndarray[ndim=1]
vector of the q values (4*pi*sin(theta)/lambda)
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awacha/sastool | sastool/fitting/standalone.py | maxwellian | def maxwellian(r, r0, n):
"""Maxwellian-like distribution of spherical particles
Inputs:
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r: np.ndarray or scalar
radii
r0: positive scalar or ErrorValue
mean radius
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"""Maxwellian-like distribution of spherical particles
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r: np.ndarray or scalar
radii
r0: positive scalar or ErrorValue
mean radius
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awacha/sastool | sastool/misc/pathutils.py | findfileindirs | def findfileindirs(filename, dirs=None, use_pythonpath=True, use_searchpath=True, notfound_is_fatal=True, notfound_val=None):
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Inputs:
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awacha/sastool | sastool/utils2d/corrections.py | twotheta | def twotheta(matrix, bcx, bcy, pixsizeperdist):
"""Calculate the two-theta matrix for a scattering matrix
Inputs:
matrix: only the shape of it is needed
bcx, bcy: beam position (counting from 0; x is row, y is column index)
pixsizeperdist: the pixel size divided by the sample-to-detecto... | python | def twotheta(matrix, bcx, bcy, pixsizeperdist):
"""Calculate the two-theta matrix for a scattering matrix
Inputs:
matrix: only the shape of it is needed
bcx, bcy: beam position (counting from 0; x is row, y is column index)
pixsizeperdist: the pixel size divided by the sample-to-detecto... | [
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awacha/sastool | sastool/utils2d/corrections.py | solidangle | def solidangle(twotheta, sampletodetectordistance, pixelsize=None):
"""Solid-angle correction for two-dimensional SAS images
Inputs:
twotheta: matrix of two-theta values
sampletodetectordistance: sample-to-detector distance
pixelsize: the pixel size in mm
The output matrix is of th... | python | def solidangle(twotheta, sampletodetectordistance, pixelsize=None):
"""Solid-angle correction for two-dimensional SAS images
Inputs:
twotheta: matrix of two-theta values
sampletodetectordistance: sample-to-detector distance
pixelsize: the pixel size in mm
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awacha/sastool | sastool/utils2d/corrections.py | solidangle_errorprop | def solidangle_errorprop(twotheta, dtwotheta, sampletodetectordistance, dsampletodetectordistance, pixelsize=None):
"""Solid-angle correction for two-dimensional SAS images with error propagation
Inputs:
twotheta: matrix of two-theta values
dtwotheta: matrix of absolute error of two-theta value... | python | def solidangle_errorprop(twotheta, dtwotheta, sampletodetectordistance, dsampletodetectordistance, pixelsize=None):
"""Solid-angle correction for two-dimensional SAS images with error propagation
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twotheta: matrix of two-theta values
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awacha/sastool | sastool/utils2d/corrections.py | angledependentabsorption | def angledependentabsorption(twotheta, transmission):
"""Correction for angle-dependent absorption of the sample
Inputs:
twotheta: matrix of two-theta values
transmission: the transmission of the sample (I_after/I_before, or
exp(-mu*d))
The output matrix is of the same shape as... | python | def angledependentabsorption(twotheta, transmission):
"""Correction for angle-dependent absorption of the sample
Inputs:
twotheta: matrix of two-theta values
transmission: the transmission of the sample (I_after/I_before, or
exp(-mu*d))
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awacha/sastool | sastool/utils2d/corrections.py | angledependentabsorption_errorprop | def angledependentabsorption_errorprop(twotheta, dtwotheta, transmission, dtransmission):
"""Correction for angle-dependent absorption of the sample with error propagation
Inputs:
twotheta: matrix of two-theta values
dtwotheta: matrix of absolute error of two-theta values
transmission: ... | python | def angledependentabsorption_errorprop(twotheta, dtwotheta, transmission, dtransmission):
"""Correction for angle-dependent absorption of the sample with error propagation
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twotheta: matrix of two-theta values
dtwotheta: matrix of absolute error of two-theta values
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awacha/sastool | sastool/utils2d/corrections.py | angledependentairtransmission | def angledependentairtransmission(twotheta, mu_air, sampletodetectordistance):
"""Correction for the angle dependent absorption of air in the scattered
beam path.
Inputs:
twotheta: matrix of two-theta values
mu_air: the linear absorption coefficient of air
sampletodetect... | python | def angledependentairtransmission(twotheta, mu_air, sampletodetectordistance):
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beam path.
Inputs:
twotheta: matrix of two-theta values
mu_air: the linear absorption coefficient of air
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awacha/sastool | sastool/utils2d/corrections.py | angledependentairtransmission_errorprop | def angledependentairtransmission_errorprop(twotheta, dtwotheta, mu_air,
dmu_air, sampletodetectordistance,
dsampletodetectordistance):
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beam path, with error propagation
Inputs:
twotheta: matrix of two-theta values
dtwotheta: absolute error matrix of two-theta
mu_air: the linear absorption coefficient of air
dmu_air: error of t... | [
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awacha/sastool | sastool/classes2/loader.py | Loader.find_file | def find_file(self, filename: str, strip_path: bool = True, what='exposure') -> str:
"""Find file in the path"""
if what == 'exposure':
path = self._path
elif what == 'header':
path = self._headerpath
elif what == 'mask':
path = self._maskpath
... | python | def find_file(self, filename: str, strip_path: bool = True, what='exposure') -> str:
"""Find file in the path"""
if what == 'exposure':
path = self._path
elif what == 'header':
path = self._headerpath
elif what == 'mask':
path = self._maskpath
... | [
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awacha/sastool | sastool/classes2/loader.py | Loader.get_subpath | def get_subpath(self, subpath: str):
"""Search a file or directory relative to the base path"""
for d in self._path:
if os.path.exists(os.path.join(d, subpath)):
return os.path.join(d, subpath)
raise FileNotFoundError | python | def get_subpath(self, subpath: str):
"""Search a file or directory relative to the base path"""
for d in self._path:
if os.path.exists(os.path.join(d, subpath)):
return os.path.join(d, subpath)
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awacha/sastool | sastool/classes2/exposure.py | Exposure.new_from_file | def new_from_file(self, filename: str, header_data: Optional[Header] = None,
mask_data: Optional[np.ndarray] = None):
"""Load an exposure from a file.""" | python | def new_from_file(self, filename: str, header_data: Optional[Header] = None,
mask_data: Optional[np.ndarray] = None):
"""Load an exposure from a file.""" | [
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awacha/sastool | sastool/classes2/exposure.py | Exposure.sum | def sum(self, only_valid=True) -> ErrorValue:
"""Calculate the sum of pixels, not counting the masked ones if only_valid is True."""
if not only_valid:
mask = 1
else:
mask = self.mask
return ErrorValue((self.intensity * mask).sum(),
((sel... | python | def sum(self, only_valid=True) -> ErrorValue:
"""Calculate the sum of pixels, not counting the masked ones if only_valid is True."""
if not only_valid:
mask = 1
else:
mask = self.mask
return ErrorValue((self.intensity * mask).sum(),
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awacha/sastool | sastool/classes2/exposure.py | Exposure.mean | def mean(self, only_valid=True) -> ErrorValue:
"""Calculate the mean of the pixels, not counting the masked ones if only_valid is True."""
if not only_valid:
intensity = self.intensity
error = self.error
else:
intensity = self.intensity[self.mask]
... | python | def mean(self, only_valid=True) -> ErrorValue:
"""Calculate the mean of the pixels, not counting the masked ones if only_valid is True."""
if not only_valid:
intensity = self.intensity
error = self.error
else:
intensity = self.intensity[self.mask]
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awacha/sastool | sastool/classes2/exposure.py | Exposure.twotheta | def twotheta(self) -> ErrorValue:
"""Calculate the two-theta array"""
row, column = np.ogrid[0:self.shape[0], 0:self.shape[1]]
rho = (((self.header.beamcentery - row) * self.header.pixelsizey) ** 2 +
((self.header.beamcenterx - column) * self.header.pixelsizex) ** 2) ** 0.5
... | python | def twotheta(self) -> ErrorValue:
"""Calculate the two-theta array"""
row, column = np.ogrid[0:self.shape[0], 0:self.shape[1]]
rho = (((self.header.beamcentery - row) * self.header.pixelsizey) ** 2 +
((self.header.beamcenterx - column) * self.header.pixelsizex) ** 2) ** 0.5
... | [
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awacha/sastool | sastool/classes2/exposure.py | Exposure.pixel_to_q | def pixel_to_q(self, row: float, column: float):
"""Return the q coordinates of a given pixel.
Inputs:
row: float
the row (vertical) coordinate of the pixel
column: float
the column (horizontal) coordinate of the pixel
Coordinates are 0-b... | python | def pixel_to_q(self, row: float, column: float):
"""Return the q coordinates of a given pixel.
Inputs:
row: float
the row (vertical) coordinate of the pixel
column: float
the column (horizontal) coordinate of the pixel
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awacha/sastool | sastool/classes2/exposure.py | Exposure.imshow | def imshow(self, *args, show_crosshair=True, show_mask=True,
show_qscale=True, axes=None, invalid_color='black',
mask_opacity=0.8, show_colorbar=True, **kwargs):
"""Plot the matrix (imshow)
Keyword arguments [and their default values]:
show_crosshair [True]: if a ... | python | def imshow(self, *args, show_crosshair=True, show_mask=True,
show_qscale=True, axes=None, invalid_color='black',
mask_opacity=0.8, show_colorbar=True, **kwargs):
"""Plot the matrix (imshow)
Keyword arguments [and their default values]:
show_crosshair [True]: if a ... | [
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show_crosshair [True]: if a cross-hair marking the beam position is
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show_mask [True]: if the mask is to be plotted.
show_qscale [True]: if the horizontal and vertical axes are to be
... | [
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awacha/sastool | sastool/classes2/exposure.py | Exposure.radial_average | def radial_average(self, qrange=None, pixel=False, returnmask=False,
errorpropagation=3, abscissa_errorpropagation=3,
raw_result=False) -> Curve:
"""Do a radial averaging
Inputs:
qrange: the q-range. If None, auto-determine. If 'linear', auto-de... | python | def radial_average(self, qrange=None, pixel=False, returnmask=False,
errorpropagation=3, abscissa_errorpropagation=3,
raw_result=False) -> Curve:
"""Do a radial averaging
Inputs:
qrange: the q-range. If None, auto-determine. If 'linear', auto-de... | [
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pixel: do a pixel-integration (instead of q)
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awacha/sastool | sastool/classes2/exposure.py | Exposure.mask_negative | def mask_negative(self):
"""Extend the mask with the image elements where the intensity is negative."""
self.mask = np.logical_and(self.mask, ~(self.intensity < 0)) | python | def mask_negative(self):
"""Extend the mask with the image elements where the intensity is negative."""
self.mask = np.logical_and(self.mask, ~(self.intensity < 0)) | [
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awacha/sastool | sastool/classes2/exposure.py | Exposure.mask_nan | def mask_nan(self):
"""Extend the mask with the image elements where the intensity is NaN."""
self.mask = np.logical_and(self.mask, ~(np.isnan(self.intensity))) | python | def mask_nan(self):
"""Extend the mask with the image elements where the intensity is NaN."""
self.mask = np.logical_and(self.mask, ~(np.isnan(self.intensity))) | [
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awacha/sastool | sastool/classes2/exposure.py | Exposure.mask_nonfinite | def mask_nonfinite(self):
"""Extend the mask with the image elements where the intensity is NaN."""
self.mask = np.logical_and(self.mask, (np.isfinite(self.intensity))) | python | def mask_nonfinite(self):
"""Extend the mask with the image elements where the intensity is NaN."""
self.mask = np.logical_and(self.mask, (np.isfinite(self.intensity))) | [
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awacha/sastool | sastool/io/credo_saxsctrl/header.py | Header.distance | def distance(self) -> ErrorValue:
"""Sample-to-detector distance"""
if 'DistCalibrated' in self._data:
dist = self._data['DistCalibrated']
else:
dist = self._data["Dist"]
if 'DistCalibratedError' in self._data:
disterr = self._data['DistCalibratedError... | python | def distance(self) -> ErrorValue:
"""Sample-to-detector distance"""
if 'DistCalibrated' in self._data:
dist = self._data['DistCalibrated']
else:
dist = self._data["Dist"]
if 'DistCalibratedError' in self._data:
disterr = self._data['DistCalibratedError... | [
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awacha/sastool | sastool/io/credo_saxsctrl/header.py | Header.temperature | def temperature(self) -> Optional[ErrorValue]:
"""Sample temperature"""
try:
return ErrorValue(self._data['Temperature'], self._data.setdefault('TemperatureError', 0.0))
except KeyError:
return None | python | def temperature(self) -> Optional[ErrorValue]:
"""Sample temperature"""
try:
return ErrorValue(self._data['Temperature'], self._data.setdefault('TemperatureError', 0.0))
except KeyError:
return None | [
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