AcquisitionParams

from mcot.mde.xps import AcquisitionParams

class mcot.mde.xps.AcquisitionParams(*args, **kwargs)

__init__(*args, **kwargs)

Inheritance diagram

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Methods

auto_update([check])	Applies all conversions and optionally check consistency in parameters
check()
clear()
copy()
from_json(filename)	Reads an XPS MDE structure from a JSON file
from_mat(filename)	Reads an XPS MDE structure from the matlab file
from_pandas(df)	Converts from a pandas dataframe to a dictionary
fromkeys([value])	Create a new dictionary with keys from iterable and values set to value.
get(key[, default])	Return the value for key if key is in the dictionary, else default.
get_index([sort_by])	Indexes the volumes based on the parameters
groupby(indices[, drop])	Groups the parameters by the indices, taking the mean for all parameters
items()
keys()
pop(k[,d])	If key is not found, d is returned if given, otherwise KeyError is raised
popitem()	Remove and return a (key, value) pair as a 2-tuple.
read(filename)	Reads the acquisition parameters from a JSON or matlab file
read_bvals_bvecs(bvals_fn[, bvecs_fn, modality])	Converts bvals/bvecs file into an MDE XPS structure
setdefault(key[, default])	Insert key with a value of default if key is not in the dictionary.
to_json(filename)	Writes an XPS MDE structure to a JSON file
to_mat(filename)	Writes an XPS MDE to a matlab file
to_pandas()	Converts to a pandas dataframe (dropping any multi-dimensional parameters)
update([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
values()
write(filename)	Writes the acquisition parameters to a JSON or matlab file

Attributes

n	Number of observations

auto_update

AcquisitionParams.auto_update(check=True)

Applies all conversions and optionally check consistency in parameters

Returns itself

check

AcquisitionParams.check()

clear

AcquisitionParams.clear() → None.  Remove all items from D.

copy

AcquisitionParams.copy() → a shallow copy of D

from_json

classmethod AcquisitionParams.from_json(filename: str) → mcot.mde.xps.AcquisitionParams

Reads an XPS MDE structure from a JSON file

Parameters

filename – .json file

Returns

XPS MDE structure

from_mat

classmethod AcquisitionParams.from_mat(filename: str) → mcot.mde.xps.AcquisitionParams

Reads an XPS MDE structure from the matlab file

Parameters

filename – .mat matlab structure produced by Markus Nilsson md-dmri library

Returns

XPS MDE structure

from_pandas

classmethod AcquisitionParams.from_pandas(df) → mcot.mde.xps.AcquisitionParams

Converts from a pandas dataframe to a dictionary

Parameters

df – pandas dataframe

Returns

fromkeys

AcquisitionParams.fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get

AcquisitionParams.get(key, default=None, /)

Return the value for key if key is in the dictionary, else default.

get_index

AcquisitionParams.get_index(sort_by=None, **parameters)

Indexes the volumes based on the parameters

Parameters

• parameters –

  mapping of parameters to how different they are allowed to be, e.g.

  • xps.get_index(b=100) groups to data into shells with b-values within 100

  • xps.get_index(b=100, te=0) ensures that only volumes with the same TE will be assigned to a given shell

  • NaNs are in the same shell, but in a different shell from everything else

• sort_by – name of the parameter to sort the indices by

Returns

(n, ) integer array with the indices (0-based)

groupby

AcquisitionParams.groupby(indices, drop=()) → mcot.mde.xps.AcquisitionParams

Groups the parameters by the indices, taking the mean for all parameters

Parameters

• indices – indices grouping observations in shells (zero-based)

• drop – parameters to drop

Returns

new acquisition parameters with one value per shell (total of max(indices) + 1)

items

AcquisitionParams.items() → a set-like object providing a view on D's items

keys

AcquisitionParams.keys() → a set-like object providing a view on D's keys

pop

AcquisitionParams.pop(k[, d]) → v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised

popitem

AcquisitionParams.popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

read

classmethod AcquisitionParams.read(filename: str)

Reads the acquisition parameters from a JSON or matlab file

Parameters

filename – filename ending with .json or .mat

Returns

the stored MDE XPS structure

read_bvals_bvecs

classmethod AcquisitionParams.read_bvals_bvecs(bvals_fn, bvecs_fn=None, modality='LTE')

Converts bvals/bvecs file into an MDE XPS structure

Parameters

• bvals_fn – file with b-values

• bvecs_fn – file with b-vectors

• modality – modality (one of LTE, PTE, or STE)

Returns

XPS object

setdefault

AcquisitionParams.setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

to_json

AcquisitionParams.to_json(filename: str)

Writes an XPS MDE structure to a JSON file

Parameters

filename – .json filename

to_mat

AcquisitionParams.to_mat(filename: str)

Writes an XPS MDE to a matlab file

Parameters

filename – .mat matlab structure readable by Markus Nilsson md-dmri library

to_pandas

AcquisitionParams.to_pandas()

Converts to a pandas dataframe (dropping any multi-dimensional parameters)

Returns

resulting dataframe

update

AcquisitionParams.update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values

AcquisitionParams.values() → an object providing a view on D's values

write

AcquisitionParams.write(filename: str)

Writes the acquisition parameters to a JSON or matlab file

Parameters

filename – filename ending with .json or .mat

Returns

the stored MDE XPS structure