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<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def vertical(x, ymin=0, ymax=1, color=None, width=None, dash=None, opacity=None): """Draws a vertical line from `ymin` to `ymax`. Parameters xmin : int, optional...
lineattr = {} if color: lineattr['color'] = color if width: lineattr['width'] = width if dash: lineattr['dash'] = dash layout = dict( shapes=[dict(type='line', x0=x, x1=x, y0=ymin, y1=ymax, opacity=opacity, line=lineattr)] ) return Chart(layout=layout)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def horizontal(y, xmin=0, xmax=1, color=None, width=None, dash=None, opacity=None): """Draws a horizontal line from `xmin` to `xmax`. Parameters xmin : int, opti...
lineattr = {} if color: lineattr['color'] = color if width: lineattr['width'] = width if dash: lineattr['dash'] = dash layout = dict( shapes=[dict(type='line', x0=xmin, x1=xmax, y0=y, y1=y, opacity=opacity, line=lineattr)] ) return Chart(layout=layout)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def line3d( x, y, z, label=None, color=None, width=None, dash=None, opacity=None, mode='lines+markers' ): """Create a 3d line chart."""
x = np.atleast_1d(x) y = np.atleast_1d(y) z = np.atleast_1d(z) assert x.shape == y.shape assert y.shape == z.shape lineattr = {} if color: lineattr['color'] = color if width: lineattr['width'] = width if dash: lineattr['dash'] = dash if y.ndim == 2: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def scatter( x=None, y=None, label=None, color=None, width=None, dash=None, opacity=None, markersize=6, yaxis=1, fill=None, text="", mode='markers', ): """Draws ...
return line( x=x, y=y, label=label, color=color, width=width, dash=dash, opacity=opacity, mode=mode, yaxis=yaxis, fill=fill, text=text, markersize=markersize, )
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def bar(x=None, y=None, label=None, mode='group', yaxis=1, opacity=None): """Create a bar chart. Parameters x : array-like, optional y : TODO, optional label : T...
assert x is not None or y is not None, "x or y must be something" yn = 'y' + str(yaxis) if y is None: y = x x = None if x is None: x = np.arange(len(y)) else: x = _try_pydatetime(x) x = np.atleast_1d(x) y = np.atleast_1d(y) if y.ndim == 2: if not ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def heatmap(z, x=None, y=None, colorscale='Viridis'): """Create a heatmap. Parameters z : TODO x : TODO, optional y : TODO, optional colorscale : TODO, optional ...
z = np.atleast_1d(z) data = [go.Heatmap(z=z, x=x, y=y, colorscale=colorscale)] return Chart(data=data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fill_zero( x=None, y=None, label=None, color=None, width=None, dash=None, opacity=None, mode='lines+markers', **kargs ): """Fill to zero. Parameters x : arra...
return line( x=x, y=y, label=label, color=color, width=width, dash=dash, opacity=opacity, mode=mode, fill='tozeroy', **kargs )
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fill_between( x=None, ylow=None, yhigh=None, label=None, color=None, width=None, dash=None, opacity=None, mode='lines+markers', **kargs ): """Fill between `y...
plot = line( x=x, y=ylow, label=label, color=color, width=width, dash=dash, opacity=opacity, mode=mode, fill=None, **kargs ) plot += line( x=x, y=yhigh, label=label, color=color, width=wi...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def rug(x, label=None, opacity=None): """Rug chart. Parameters x : array-like, optional label : TODO, optional opacity : TODO, optional Returns ------- Chart """
x = _try_pydatetime(x) x = np.atleast_1d(x) data = [ go.Scatter( x=x, y=np.ones_like(x), name=label, opacity=opacity, mode='markers', marker=dict(symbol='line-ns-open'), ) ] layout = dict( barmode='overl...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def surface(x, y, z): """Surface plot. Parameters x : array-like, optional y : array-like, optional z : array-like, optional Returns ------- Chart """
data = [go.Surface(x=x, y=y, z=z)] return Chart(data=data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def hist2d(x, y, label=None, opacity=None): """2D Histogram. Parameters x : array-like, optional y : array-like, optional label : TODO, optional opacity : float,...
x = np.atleast_1d(x) y = np.atleast_1d(y) data = [go.Histogram2d(x=x, y=y, opacity=opacity, name=label)] return Chart(data=data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ytickangle(self, angle, index=1): """Set the angle of the y-axis tick labels. Parameters value : int Angle in degrees index : int, optional Y-axis index Retu...
self.layout['yaxis' + str(index)]['tickangle'] = angle return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ylabelsize(self, size, index=1): """Set the size of the label. Parameters size : int Returns ------- Chart """
self.layout['yaxis' + str(index)]['titlefont']['size'] = size return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def yticksize(self, size, index=1): """Set the tick font size. Parameters size : int Returns ------- Chart """
self.layout['yaxis' + str(index)]['tickfont']['size'] = size return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ytickvals(self, values, index=1): """Set the tick values. Parameters values : array-like Returns ------- Chart """
self.layout['yaxis' + str(index)]['tickvals'] = values return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def yticktext(self, labels, index=1): """Set the tick labels. Parameters labels : array-like Returns ------- Chart """
self.layout['yaxis' + str(index)]['ticktext'] = labels return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ylim(self, low, high, index=1): """Set yaxis limits. Parameters low : number high : number index : int, optional Returns ------- Chart """
self.layout['yaxis' + str(index)]['range'] = [low, high] return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ydtick(self, dtick, index=1): """Set the tick distance."""
self.layout['yaxis' + str(index)]['dtick'] = dtick return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ynticks(self, nticks, index=1): """Set the number of ticks."""
self.layout['yaxis' + str(index)]['nticks'] = nticks return self
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def show( self, filename: Optional[str] = None, show_link: bool = True, auto_open: bool = True, detect_notebook: bool = True, ) -> None: """Display the chart. Par...
kargs = {} if detect_notebook and _detect_notebook(): py.init_notebook_mode() plot = py.iplot else: plot = py.plot if filename is None: filename = NamedTemporaryFile(prefix='plotly', suffix='.html', delete=False).name k...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save( self, filename: Optional[str] = None, show_link: bool = True, auto_open: bool = False, output: str = 'file', plotlyjs: bool = True, ) -> str: """Save th...
if filename is None: filename = NamedTemporaryFile(prefix='plotly', suffix='.html', delete=False).name # NOTE: this doesn't work for output 'div' py.plot( self, show_link=show_link, filename=filename, auto_open=auto_open, o...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_method_sig(method): """ Given a function, it returns a string that pretty much looks how the function signature_ would be written in python. :param metho...
# The return value of ArgSpec is a bit weird, as the list of arguments and # list of defaults are returned in separate array. # eg: ArgSpec(args=['first_arg', 'second_arg', 'third_arg'], # varargs=None, keywords=None, defaults=(42, 'something')) argspec = inspect.getargspec(method) arg_index=0...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ThenAt(self, n, f, *_args, **kwargs): """ `ThenAt` enables you to create a partially apply many arguments to a function, the returned partial expects a singl...
_return_type = None n_args = n - 1 if '_return_type' in kwargs: _return_type = kwargs['_return_type'] del kwargs['_return_type'] @utils.lift def g(x): new_args = _args[0:n_args] + (x,) + _args[n_args:] if n_args >= 0 else _args ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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, it...
fs = [ _parse(elem)._f for elem in sequence ] def g(x, state): return functools.reduce(lambda args, f: f(*args), fs, (x, state)) return self.__then__(g, **kwargs)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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)) if len(state_dict) > 1: raise Exception("Please include at-most 1 keyword argument expression, got {0}".format(state_dict)) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 le...
if until is None: return sum(1 for _ in GraphemeIterator(string)) iterator = graphemes(string) count = 0 while True: try: if count >= until: break next(iterator) except StopIteration: break else: count += 1...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def slice(string, start=None, end=None): """ Returns a substring of the given string, counting graphemes instead of codepoints. Negative indices is currently not...
if start is None: start = 0 if end is not None and start >= end: return "" if start < 0: raise NotImplementedError("Negative indexing is currently not supported.") sum_ = 0 start_index = None for grapheme_index, grapheme_length in enumerate(grapheme_lengths(string)): ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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` o...
if substring not in string: return False substr_graphemes = list(graphemes(substring)) if len(substr_graphemes) == 0: return True elif len(substr_graphemes) == 1: return substr_graphemes[0] in graphemes(string) else: str_iter = graphemes(string) str_sub_par...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 string.startswith(prefix) and safe_split_index(string, len(prefix)) == len(prefix)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 ...
expected_index = len(string) - len(suffix) return string.endswith(suffix) and safe_split_index(string, expected_index) == expected_index
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def safe_split_index(string, max_len): """ Returns the highest index up to `max_len` at which the given string can be sliced, without breaking a grapheme. This i...
last_index = get_last_certain_break_index(string, max_len) for l in grapheme_lengths(string[last_index:]): if last_index + l > max_len: break last_index += l return last_index
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def writeB1logfile(filename, data): """Write a header structure into a B1 logfile. Inputs: filename: name of the file. data: header dictionary Notes: exceptions ...
allkeys = list(data.keys()) f = open(filename, 'wt', encoding='utf-8') for ld in _logfile_data: # process each line linebegin = ld[0] fieldnames = ld[1] # set the default formatter if it is not given if len(ld) < 3: formatter = str elif ld[2] is None: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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: try: right = f(right) break except ValueError: continue return r...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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(16) for i in range(29)] return {'Xsize': intheader[0], 'Ysize': intheader[1], 'M...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def Square(x, a, b, c): """Second order polynomial Inputs: ------- ``x``: independent variable ``a``: coefficient of the second-order term ``b``: coefficient of ...
return a * x ** 2 + b * x + c
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def Cube(x, a, b, c, d): """Third order polynomial Inputs: ------- ``x``: independent variable ``a``: coefficient of the third-order term ``b``: coefficient of t...
return a * x ** 3 + b * x ** 2 + c * x + d
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def LogNormal(x, a, mu, sigma): """PDF of a log-normal distribution Inputs: ------- ``x``: independent variable ``a``: amplitude ``mu``: center parameter ``sigma...
return a / np.sqrt(2 * np.pi * sigma ** 2 * x ** 2) *\ np.exp(-(np.log(x) - mu) ** 2 / (2 * sigma ** 2))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def find_subdirs(startdir='.', recursion_depth=None): """Find all subdirectory of a directory. Inputs: startdir: directory to start with. Defaults to the current...
startdir = os.path.expanduser(startdir) direct_subdirs = [os.path.join(startdir, x) for x in os.listdir( startdir) if os.path.isdir(os.path.join(startdir, x))] if recursion_depth is None: next_recursion_depth = None else: next_recursion_depth = recursion_depth - 1 if (recurs...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 vec...
if Nfit is None: Nfit = N # find points where the curve grows for N points before them and # decreases for N points after them. To accomplish this, we create # an indicator array of the sign of the first derivative. sgndiff = np.sign(np.diff(y)) xdiff = x[:-1] # associate difference va...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 ...
with open(filename, 'rt') as f: sf = {'motors': [], 'maxscannumber': 0} sf['originalfilename'] = filename lastscannumber = None while True: l = f.readline() if l.startswith('#F'): sf['filename'] = l[2:].strip() elif l.startswith('#...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def energy(self) -> ErrorValue: """X-ray energy"""
return (ErrorValue(*(scipy.constants.physical_constants['speed of light in vacuum'][0::2])) * ErrorValue(*(scipy.constants.physical_constants['Planck constant in eV s'][0::2])) / scipy.constants.nano / self.wavelength)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 wit...
# for each row and column find the center of gravity data1 = data.copy() # take a copy, because elements will be tampered with data1[mask == 0] = 0 # set masked elements to zero # vector of x (row) coordinates x = np.arange(data1.shape[0]) # vector of y (column) coordinates y = np.arange(...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def findbeam_slices(data, orig_initial, mask=None, maxiter=0, epsfcn=0.001, dmin=0, dmax=np.inf, sector_width=np.pi / 9.0, extent=10, callback=None): """Find bea...
if mask is None: mask = np.ones(data.shape) data = data.astype(np.double) def targetfunc(orig, data, mask, orig_orig, callback): # integrate four sectors I = [None] * 4 p, Ints, A = radint_nsector(data, None, -1, -1, -1, orig[0] + orig_orig[0], orig[1] + orig_orig[1], mask=...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def findbeam_azimuthal(data, orig_initial, mask=None, maxiter=100, Ntheta=50, dmin=0, dmax=np.inf, extent=10, callback=None): """Find beam center using azimuthal...
if mask is None: mask = np.ones(data.shape) data = data.astype(np.double) def targetfunc(orig, data, mask, orig_orig, callback): def sinfun(p, x, y): return (y - np.sin(x + p[1]) * p[0] - p[2]) / np.sqrt(len(x)) t, I, a = azimintpix(data, None, orig[ ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 azim...
if Ntheta % 2: raise ValueError('Ntheta should be even!') if mask is None: mask = np.ones_like(data).astype(np.uint8) data = data.astype(np.double) # the function to minimize is the sum of squared difference of two halves of # the azimuthal integral. def targetfunc(orig, data, ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def findbeam_semitransparent(data, pri, threshold=0.05): """Find beam with 2D weighting of semitransparent beamstop area Inputs: data: scattering matrix pri: lis...
rowmin = np.floor(min(pri[2:])) rowmax = np.ceil(max(pri[2:])) colmin = np.floor(min(pri[:2])) colmax = np.ceil(max(pri[:2])) if threshold is not None: # beam area on the scattering image B = data[rowmin:rowmax, colmin:colmax] # print B.shape # row and column indice...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def findbeam_radialpeak(data, orig_initial, mask, rmin, rmax, maxiter=100, drive_by='amplitude', extent=10, callback=None): """Find the beam by minimizing the wi...
orig_initial = np.array(orig_initial) mask = 1 - mask.astype(np.uint8) data = data.astype(np.double) pix = np.arange(rmin * 1.0, rmax * 1.0, 1) if drive_by.lower() == 'hwhm': def targetfunc(orig, data, mask, orig_orig, callback): I = radintpix( data, None, orig[0...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 on...
if qmin is None: qmin = max(self.q.min(), other.q.min()) if qmax is None: xmax = min(self.q.max(), other.q.max()) data1 = self.trim(qmin, qmax) data2 = other.trim(qmin, qmax) if Npoints is None: Npoints = min(len(data1), len(data2)) co...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 self._fixed_parameters[i] is not None] indices_of_free_parameters = [i for i in range(len(self....
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def writeint2dnorm(filename, Intensity, Error=None): """Save the intensity and error matrices to a file Inputs ------ filename: string the name of the file Inten...
whattosave = {'Intensity': Intensity} if Error is not None: whattosave['Error'] = Error if filename.upper().endswith('.NPZ'): np.savez(filename, **whattosave) elif filename.upper().endswith('.MAT'): scipy.io.savemat(filename, whattosave) else: # text file np.savetxt...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def readbdfv2(filename, bdfext='.bdf', bhfext='.bhf'): """Read a version 2 Bessy Data File Inputs ------ filename: string the name of the input file. One can giv...
datas = header.readbhfv2(filename, True, bdfext, bhfext) return datas
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def readmar(filename): """Read a two-dimensional scattering pattern from a MarResearch .image file. """
hed = header.readmarheader(filename) with open(filename, 'rb') as f: h = f.read(hed['recordlength']) data = np.fromstring( f.read(2 * hed['Xsize'] * hed['Ysize']), '<u2').astype(np.float64) if hed['highintensitypixels'] > 0: raise NotImplementedError( ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def writebdfv2(filename, bdf, bdfext='.bdf', bhfext='.bhf'): """Write a version 2 Bessy Data File Inputs ------ filename: string the name of the output file. One...
if filename.endswith(bdfext): basename = filename[:-len(bdfext)] elif filename.endswith(bhfext): basename = filename[:-len(bhfext)] else: basename = filename header.writebhfv2(basename + '.bhf', bdf) f = open(basename + '.bdf', 'wb') keys = ['RAWDATA', 'RAWERROR', 'CORRD...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fill_padding(padded_string): # type: (bytes) -> bytes """ Fill up missing padding in a string. This function makes sure that the string has length which is m...
length = len(padded_string) reminder = len(padded_string) % 4 if reminder: return padded_string.ljust(length + 4 - reminder, b'.') return padded_string
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def decode(encoded): # type: (bytes) -> bytes """ Decode the result of querystringsafe_base64_encode or a regular base64. .. note :: As a regular base64 string d...
padded_string = fill_padding(encoded) return urlsafe_b64decode(padded_string.replace(b'.', b'='))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def flatten_hierarchical_dict(original_dict, separator='.', max_recursion_depth=None): """Flatten a dict. Inputs ------ original_dict: dict the dictionary to fla...
if max_recursion_depth is not None and max_recursion_depth <= 0: # we reached the maximum recursion depth, refuse to go further return original_dict if max_recursion_depth is None: next_recursion_depth = None else: next_recursion_depth = max_recursion_depth - 1 dict1 = {...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fit_shullroess(q, Intensity, Error, R0=None, r=None): """Do a Shull-Roess fitting on the scattering data. Inputs: q: np.ndarray[ndim=1] vector of the q value...
q = np.array(q) Intensity = np.array(Intensity) Error = np.array(Error) if R0 is None: r0s = np.linspace(1, 2 * np.pi / q.min(), 1000) def naive_fit_chi2(q, Intensity, r0): p = np.polyfit(np.log(q ** 2 + 3 / r0 ** 2), np.log(Intensity), 1) return ((np.polyval(p, ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def findfileindirs(filename, dirs=None, use_pythonpath=True, use_searchpath=True, notfound_is_fatal=True, notfound_val=None): """Find file in multiple directorie...
if os.path.isabs(filename): if os.path.exists(filename): return filename elif notfound_is_fatal: raise IOError('File ' + filename + ' not found.') else: return notfound_val if dirs is None: dirs = [] dirs = normalize_listargument(dirs) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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...
col, row = np.meshgrid(list(range(matrix.shape[1])), list(range(matrix.shape[0]))) return np.arctan(np.sqrt((row - bcx) ** 2 + (col - bcy) ** 2) * pixsizeperdist)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def solidangle(twotheta, sampletodetectordistance, pixelsize=None): """Solid-angle correction for two-dimensional SAS images Inputs: twotheta: matrix of two-thet...
if pixelsize is None: pixelsize = 1 return sampletodetectordistance ** 2 / np.cos(twotheta) ** 3 / pixelsize ** 2
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def solidangle_errorprop(twotheta, dtwotheta, sampletodetectordistance, dsampletodetectordistance, pixelsize=None): """Solid-angle correction for two-dimensional...
SAC = solidangle(twotheta, sampletodetectordistance, pixelsize) if pixelsize is None: pixelsize = 1 return (SAC, (sampletodetectordistance * (4 * dsampletodetectordistance ** 2 * np.cos(twotheta) ** 2 + 9 * dtwotheta ** 2 * sampletodetectordistanc...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def angledependentabsorption(twotheta, transmission): """Correction for angle-dependent absorption of the sample Inputs: twotheta: matrix of two-theta values tra...
cor = np.ones(twotheta.shape) if transmission == 1: return cor mud = -np.log(transmission) cor[twotheta > 0] = transmission * mud * (1 - 1 / np.cos(twotheta[twotheta > 0])) / (np.exp(-mud / np.cos(twotheta[twotheta > 0])) - np.exp(-mud)) return cor
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def angledependentabsorption_errorprop(twotheta, dtwotheta, transmission, dtransmission): """Correction for angle-dependent absorption of the sample with error p...
# error propagation formula calculated using sympy return (angledependentabsorption(twotheta, transmission), _calc_angledependentabsorption_error(twotheta, dtwotheta, transmission, dtransmission))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def angledependentairtransmission(twotheta, mu_air, sampletodetectordistance): """Correction for the angle dependent absorption of air in the scattered beam path...
return np.exp(mu_air * sampletodetectordistance / np.cos(twotheta))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def angledependentairtransmission_errorprop(twotheta, dtwotheta, mu_air, dmu_air, sampletodetectordistance, dsampletodetectordistance): """Correction for the ang...
return (np.exp(mu_air * sampletodetectordistance / np.cos(twotheta)), np.sqrt(dmu_air ** 2 * sampletodetectordistance ** 2 * np.exp(2 * mu_air * sampletodetectordistance / np.cos(twotheta)) / np.cos(twotheta) ** 2 + dsampletodetectordistance ** 2 * ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 else: path = self._path tried = [] if strip_path: filename = os.path.split(filen...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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(), ((self.error * mask) ** 2).sum() ** 0.5)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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] error = self.error[self.mask] return ErrorValue(intensity.mean(), (error ** 2).mean() ** 0.5)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 assert isinstance(self.header.pixelsizex, ErrorValue) assert isinst...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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 colu...
qrow = 4 * np.pi * np.sin( 0.5 * np.arctan( (row - float(self.header.beamcentery)) * float(self.header.pixelsizey) / float(self.header.distance))) / float(self.header.wavelength) qcol = 4 * np.pi * np.sin(0.5 * np.arctan( (colu...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def radial_average(self, qrange=None, pixel=False, returnmask=False, errorpropagation=3, abscissa_errorpropagation=3, raw_result=False) -> Curve: """Do a radial a...
retmask = None if isinstance(qrange, str): if qrange == 'linear': qrange = None autoqrange_linear = True elif qrange == 'log': qrange = None autoqrange_linear = False else: raise ValueErr...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: 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'] elif 'DistError' in self._data: disterr = self._data...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def simultaneous_nonlinear_leastsquares(xs, ys, dys, func, params_inits, verbose=False, **kwargs): """Do a simultaneous nonlinear least-squares fit and return th...
p, dp, statdict = simultaneous_nlsq_fit(xs, ys, dys, func, params_inits, verbose, **kwargs) params = [[ErrorValue(p_, dp_) for (p_, dp_) in zip(pcurrent, dpcurrent)] for (pcurrent, dpcurrent) in zip(p, dp)] return tuple(params + [statdict])
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def tostring(self: 'ErrorValue', extra_digits: int = 0, plusminus: str = ' +/- ', fmt: str = None) -> str: """Make a string representation of the value and its un...
if isinstance(fmt, str) and fmt.lower().endswith('tex'): return re.subn('(\d*)(\.(\d)*)?[eE]([+-]?\d+)', lambda m: (r'$%s%s\cdot 10^{%s}$' % (m.group(1), m.group(2), m.group(4))).replace('None', ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def evalfunc(cls, func, *args, **kwargs): """Evaluate a function with error propagation. Inputs: ------- ``func``: callable this is the function to be evaluated....
def do_random(x): if isinstance(x, cls): return x.random() else: return x if 'NMC' not in kwargs: kwargs['NMC'] = 1000 if 'exceptions_to_skip' not in kwargs: kwargs['exceptions_to_skip'] = [] if 'exception...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def GeneralGuinier(q, G, Rg, s): """Generalized Guinier scattering Inputs: ------- ``q``: independent variable ``G``: factor ``Rg``: radius of gyration ``s``: di...
return G / q ** (3 - s) * np.exp(-(q * Rg) ** 2 / s)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def GuinierPorod(q, G, Rg, alpha): """Empirical Guinier-Porod scattering Inputs: ------- ``q``: independent variable ``G``: factor of the Guinier-branch ``Rg``: ...
return GuinierPorodMulti(q, G, Rg, alpha)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def PorodGuinier(q, a, alpha, Rg): """Empirical Porod-Guinier scattering Inputs: ------- ``q``: independent variable ``a``: factor of the power-law branch ``alph...
return PorodGuinierMulti(q, a, alpha, Rg)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def PorodGuinierPorod(q, a, alpha, Rg, beta): """Empirical Porod-Guinier-Porod scattering Inputs: ------- ``q``: independent variable ``a``: factor of the first ...
return PorodGuinierMulti(q, a, alpha, Rg, beta)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def GuinierPorodGuinier(q, G, Rg1, alpha, Rg2): """Empirical Guinier-Porod-Guinier scattering Inputs: ------- ``q``: independent variable ``G``: factor for the f...
return GuinierPorodMulti(q, G, Rg1, alpha, Rg2)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def DampedPowerlaw(q, a, alpha, sigma): """Damped power-law Inputs: ------- ``q``: independent variable ``a``: factor ``alpha``: exponent ``sigma``: hwhm of the ...
return a * q ** alpha * np.exp(-q ** 2 / (2 * sigma ** 2))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def PowerlawGuinierPorodConst(q, A, alpha, G, Rg, beta, C): """Sum of a Power-law, a Guinier-Porod curve and a constant. Inputs: ------- ``q``: independent varia...
return PowerlawPlusConstant(q, A, alpha, C) + GuinierPorod(q, G, Rg, beta)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def GuinierPorodMulti(q, G, *Rgsalphas): """Empirical multi-part Guinier-Porod scattering Inputs: ------- ``q``: independent variable ``G``: factor for the first...
scalefactor = G funcs = [lambda q: Guinier(q, G, Rgsalphas[0])] indices = np.ones_like(q, dtype=np.bool) constraints = [] for i in range(1, len(Rgsalphas)): if i % 2: # Rgsalphas[i] is an exponent, Rgsalphas[i-1] is a radius of gyration qsep = _PGgen_qsep(Rgsalphas[i...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def PorodGuinierMulti(q, A, *alphasRgs): """Empirical multi-part Porod-Guinier scattering Inputs: ------- ``q``: independent variable ``A``: factor for the first...
scalefactor = A funcs = [lambda q: Powerlaw(q, A, alphasRgs[0])] indices = np.ones_like(q, dtype=np.bool) constraints = [] for i in range(1, len(alphasRgs)): if i % 2: # alphasRgs[i] is a radius of gyration, alphasRgs[i-1] is a power-law exponent qsep = _PGgen_qsep(a...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def GeneralGuinierPorod(q, factor, *args, **kwargs): """Empirical generalized multi-part Guinier-Porod scattering Inputs: ------- ``q``: independent variable ``f...
if kwargs.get('startswithguinier', True): funcs = [lambda q, A = factor:GeneralGuinier(q, A, args[0], args[1])] i = 2 guiniernext = False else: funcs = [lambda q, A = factor: Powerlaw(q, A, args[0])] i = 1 guiniernext = True indices = np.ones_like(q, dtype=np...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def ExcludedVolumeChain(q, Rg, nu): """Scattering intensity of a generalized excluded-volume Gaussian chain Inputs: ------- ``q``: independent variable ``Rg``: r...
u = (q * Rg) ** 2 * (2 * nu + 1) * (2 * nu + 2) / 6. return (u ** (0.5 / nu) * gamma(0.5 / nu) * gammainc(0.5 / nu, u) - gamma(1. / nu) * gammainc(1. / nu, u)) / (nu * u ** (1. / nu))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def BorueErukhimovich(q, C, r0, s, t): """Borue-Erukhimovich model of microphase separation in polyelectrolytes Inputs: ------- ``q``: independent variable ``C``...
x = q * r0 return C * (x ** 2 + s) / ((x ** 2 + s) * (x ** 2 + t) + 1)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def BorueErukhimovich_Powerlaw(q, C, r0, s, t, nu): """Borue-Erukhimovich model ending in a power-law. Inputs: ------- ``q``: independent variable ``C``: scaling...
def get_xsep(alpha, s, t): A = alpha + 2 B = 2 * s * alpha + t * alpha + 4 * s C = s * t * alpha + alpha + alpha * s ** 2 + alpha * s * t - 2 + 2 * s ** 2 D = alpha * s ** 2 * t + alpha * s r = np.roots([A, B, C, D]) #print "get_xsep: ", alpha, s, t, r return...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def sample(self, data, interval): '''Sample a patch from the data object Parameters ---------- data : dict A data dict as produced by pumpp.Pump.transform interval : slice The time interval to sample Returns ------- data_slice : ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def indices(self, data): '''Generate patch start indices Parameters ---------- data : dict of np.ndarray As produced by pumpp.transform Yields ------ start : int >= 0 The start index of a sample patch ''' duration = self.d...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def scope(self, key): '''Apply the name scope to a key Parameters ---------- key : string Returns ------- `name/key` if `name` is not `None`; otherwise, `key`. ''' if self.name is None: return key return '{:s}/{:s}'.fo...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def register(self, field, shape, dtype): '''Register a field as a tensor with specified shape and type. A `Tensor` of the given shape and type will be registered in this object's `fields` dict. Parameters ---------- field : str The name of the field ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def merge(self, data): '''Merge an array of output dictionaries into a single dictionary with properly scoped names. Parameters ---------- data : list of dict Output dicts as produced by `pumpp.task.BaseTaskTransformer.transform` or `pumpp.feature.Feature...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def add(self, operator): '''Add an operator to the Slicer Parameters ---------- operator : Scope (TaskTransformer or FeatureExtractor) The new operator to add ''' if not isinstance(operator, Scope): raise ParameterError('Operator {} must be a Task...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description:
def data_duration(self, data): '''Compute the valid data duration of a dict Parameters ---------- data : dict As produced by pumpp.transform Returns ------- length : int The minimum temporal extent of a dynamic observation in data ...