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\title{pyM2aia}
\date{Mar 15, 2024}
\release{}
\author{Jonas Cordes}
\newcommand{\sphinxlogo}{\vbox{}}
\renewcommand{\releasename}{}
\makeindex
\begin{document}

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\pagestyle{empty}
\sphinxmaketitle
\pagestyle{plain}
\sphinxtableofcontents
\pagestyle{normal}
\phantomsection\label{\detokenize{index::doc}}

\begin{description}
\sphinxlineitem{m2aia.Dataset module}
\end{description}
\index{module@\spxentry{module}!m2aia.Dataset@\spxentry{m2aia.Dataset}}\index{m2aia.Dataset@\spxentry{m2aia.Dataset}!module@\spxentry{module}}\index{BaseDataSet (class in m2aia.Dataset)@\spxentry{BaseDataSet}\spxextra{class in m2aia.Dataset}}\phantomsection\label{\detokenize{index:module-m2aia.Dataset}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.BaseDataSet}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{class\DUrole{w}{ }}}\sphinxcode{\sphinxupquote{m2aia.Dataset.}}\sphinxbfcode{\sphinxupquote{BaseDataSet}}}{\sphinxparam{\DUrole{n}{images}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List\DUrole{p}{{[}}{\hyperref[\detokenize{index:m2aia.ImageIO.ImzMLReader}]{\sphinxcrossref{ImzMLReader}}}\DUrole{p}{{]}}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{buffer\_type}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{str}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Bases: \sphinxcode{\sphinxupquote{object}}
\index{getitems() (m2aia.Dataset.BaseDataSet method)@\spxentry{getitems()}\spxextra{m2aia.Dataset.BaseDataSet method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.BaseDataSet.getitems}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{getitems}}}{\sphinxparam{\DUrole{n}{indexes}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List\DUrole{p}{{[}}int\DUrole{p}{{]}}}}}{}
\pysigstopsignatures
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\end{fulllineitems}

\index{IonImageDataset (class in m2aia.Dataset)@\spxentry{IonImageDataset}\spxextra{class in m2aia.Dataset}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.IonImageDataset}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{class\DUrole{w}{ }}}\sphinxcode{\sphinxupquote{m2aia.Dataset.}}\sphinxbfcode{\sphinxupquote{IonImageDataset}}}{\sphinxparam{\DUrole{n}{images}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List\DUrole{p}{{[}}{\hyperref[\detokenize{index:m2aia.ImageIO.ImzMLReader}]{\sphinxcrossref{ImzMLReader}}}\DUrole{p}{{]}}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{centroids}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List\DUrole{p}{{[}}float\DUrole{p}{{]}}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{tolerance}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{float}}\sphinxparamcomma \sphinxparam{\DUrole{n}{tolerance\_type}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{str}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{\textquotesingle{}ppm\textquotesingle{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{buffer\_type}\DUrole{o}{=}\DUrole{default_value}{\textquotesingle{}memory\textquotesingle{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{transforms}\DUrole{o}{=}\DUrole{default_value}{None}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Bases: {\hyperref[\detokenize{index:m2aia.Dataset.BaseDataSet}]{\sphinxcrossref{\sphinxcode{\sphinxupquote{BaseDataSet}}}}}
\index{get\_tolerance() (m2aia.Dataset.IonImageDataset method)@\spxentry{get\_tolerance()}\spxextra{m2aia.Dataset.IonImageDataset method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.IonImageDataset.get_tolerance}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{get\_tolerance}}}{\sphinxparam{\DUrole{n}{c}}}{}
\pysigstopsignatures
\end{fulllineitems}

\index{getitems() (m2aia.Dataset.IonImageDataset method)@\spxentry{getitems()}\spxextra{m2aia.Dataset.IonImageDataset method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.IonImageDataset.getitems}}
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\pysigstopsignatures
\end{fulllineitems}

\index{make\_buffered\_image() (m2aia.Dataset.IonImageDataset method)@\spxentry{make\_buffered\_image()}\spxextra{m2aia.Dataset.IonImageDataset method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.IonImageDataset.make_buffered_image}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{make\_buffered\_image}}}{\sphinxparam{\DUrole{n}{index}}}{}
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\end{fulllineitems}


\end{fulllineitems}

\index{SpectrumDataset (class in m2aia.Dataset)@\spxentry{SpectrumDataset}\spxextra{class in m2aia.Dataset}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.SpectrumDataset}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{class\DUrole{w}{ }}}\sphinxcode{\sphinxupquote{m2aia.Dataset.}}\sphinxbfcode{\sphinxupquote{SpectrumDataset}}}{\sphinxparam{images: \textasciitilde{}typing.List{[}\textasciitilde{}m2aia.ImageIO.ImzMLReader{]}, labeled\_images: \textasciitilde{}typing.List{[}\textasciitilde{}numpy.array{]} | None = None, sampling\_masks: \textasciitilde{}typing.List{[}\textasciitilde{}numpy.array{]} | None = None, spectrum\_mask\_indices: \textasciitilde{}typing.List{[}int{]} | None = None, tolerance: \textasciitilde{}numpy.float32 | None = None, is\_tolerance\_in\_ppm: bool = True, label\_map: \textasciitilde{}typing.Dict | None = None, shape: \textasciitilde{}typing.Tuple | None = None, transform\_data=None, transform\_labels=None, buffer\_type: str = \textquotesingle{}memory\textquotesingle{}, reduce\_function=\textless{}function mean\textgreater{}, shuffle=False, quiet\_init=True}}{}
\pysigstopsignatures
\sphinxAtStartPar
Bases: {\hyperref[\detokenize{index:m2aia.Dataset.BaseDataSet}]{\sphinxcrossref{\sphinxcode{\sphinxupquote{BaseDataSet}}}}}

\sphinxAtStartPar
Dataset for accession individual spectra and class labels (optional) of multiple images (m2aia.ImzMLReader objects).

\sphinxAtStartPar
The aim of the SpectrumDataset is to provide convenient access to spectra of single or multiple ImzMLReaders.
Two access strategy exist:
1) Spectral approach: a single spectrum is returned.
2) Spatio\sphinxhyphen{}spectral: a central spectrum and corresponding neighbors are returned.

\sphinxAtStartPar
To use multiple images a spectra depth of equal size for each image is required.

\sphinxAtStartPar
A label mask can be provided and is used to return labels for each accessed element.

\sphinxAtStartPar
To use the spatio\sphinxhyphen{}spectral approach, a shape element is required. The Dataset will then return
the spectrum embedded in neighboring spectra, i.e. if the shape tuple is shape=(5,5) the shape of a
data entry is {[}B,C,H,W{]}, with batchsize as B = 1, spectrum depth as C = len(spectrum), width
as W=5 and height as H=5 of the patch.

\sphinxAtStartPar
If no shape element was provided, the Dataset will return a single spectrum with shape {[}B=1,C{]}.

\sphinxAtStartPar
If multiple elements of the Dataset should be queried at one, the SpectrumDataset.getitems(list\_of\_indices)
returns a batch like object containing the elements. i.e. without a shape definition returned elements will have
the shape {[}B=len(list\_of\_indices), C{]} and with shape=(5,5) the shape {[}B=len(list\_of\_indices),C,H=5,W=5{]}.
This is used in m2aia.BatchGenerator.

\sphinxAtStartPar
Complete processing examples with focus on deep learning can be found on \sphinxurl{https://github.com/m2aia/pym2aia-examples}

\sphinxAtStartPar
Example usage:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{k+kn}{import} \PYG{n+nn}{m2aia} \PYG{k}{as} \PYG{n+nn}{m2}

\PYG{n}{I} \PYG{o}{=} \PYG{n}{m2}\PYG{o}{.}\PYG{n}{ImzMLReader}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{path/to/imzMl/file.imzML}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{SetNormalization}\PYG{p}{(}\PYG{n}{m2}\PYG{o}{.}\PYG{n}{m2NormalizationTIC}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{SetIntensityTransformation}\PYG{p}{(}\PYG{n}{m2}\PYG{o}{.}\PYG{n}{m2IntensityTransformationSquareRoot}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{Execute}\PYG{p}{(}\PYG{p}{)}

\PYG{n}{dataset} \PYG{o}{=} \PYG{n}{m2}\PYG{o}{.}\PYG{n}{SpectrumDataset}\PYG{p}{(}\PYG{p}{[}\PYG{n}{I}\PYG{p}{]}\PYG{p}{,} \PYG{n}{shuffle}\PYG{o}{=}\PYG{k+kc}{True}\PYG{p}{)}
\PYG{k}{for} \PYG{n}{X}\PYG{p}{,}\PYG{n}{Y} \PYG{o+ow}{in} \PYG{n}{dataset}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
    \PYG{n+nb}{print}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{Spectrum}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{X}\PYG{o}{.}\PYG{n}{shape}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{Class Labels}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{Y}\PYG{o}{.}\PYG{n}{shape}\PYG{p}{)}
    \PYG{n}{do\PYGZus{}something}\PYG{p}{(}\PYG{n}{X}\PYG{p}{,}\PYG{n}{Y}\PYG{p}{)}
\end{sphinxVerbatim}
\index{find\_nearest\_indices() (m2aia.Dataset.SpectrumDataset method)@\spxentry{find\_nearest\_indices()}\spxextra{m2aia.Dataset.SpectrumDataset method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.SpectrumDataset.find_nearest_indices}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{find\_nearest\_indices}}}{\sphinxparam{\DUrole{n}{centroids}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{array}}\sphinxparamcomma \sphinxparam{\DUrole{n}{xaxis}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{array}}}{}
\pysigstopsignatures
\end{fulllineitems}

\index{find\_subrange\_indices() (m2aia.Dataset.SpectrumDataset method)@\spxentry{find\_subrange\_indices()}\spxextra{m2aia.Dataset.SpectrumDataset method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.SpectrumDataset.find_subrange_indices}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{find\_subrange\_indices}}}{\sphinxparam{\DUrole{n}{xs}}\sphinxparamcomma \sphinxparam{\DUrole{n}{center\_index}}\sphinxparamcomma \sphinxparam{\DUrole{n}{tolerance}}\sphinxparamcomma \sphinxparam{\DUrole{n}{is\_ppm}}}{}
\pysigstopsignatures
\end{fulllineitems}

\index{getitems() (m2aia.Dataset.SpectrumDataset method)@\spxentry{getitems()}\spxextra{m2aia.Dataset.SpectrumDataset method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Dataset.SpectrumDataset.getitems}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{getitems}}}{\sphinxparam{\DUrole{n}{dataset\_query\_indices}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List\DUrole{p}{{[}}int\DUrole{p}{{]}}}}}{}
\pysigstopsignatures
\end{fulllineitems}


\end{fulllineitems}



\chapter{m2aia.Generators module}
\label{\detokenize{index:m2aia-generators-module}}\begin{quote}
\index{module@\spxentry{module}!m2aia.Generators@\spxentry{m2aia.Generators}}\index{m2aia.Generators@\spxentry{m2aia.Generators}!module@\spxentry{module}}\index{BatchGenerator (class in m2aia.Generators)@\spxentry{BatchGenerator}\spxextra{class in m2aia.Generators}}\phantomsection\label{\detokenize{index:module-m2aia.Generators}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Generators.BatchGenerator}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{class\DUrole{w}{ }}}\sphinxcode{\sphinxupquote{m2aia.Generators.}}\sphinxbfcode{\sphinxupquote{BatchGenerator}}}{\sphinxparam{\DUrole{n}{dataset}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{{\hyperref[\detokenize{index:m2aia.Dataset.BaseDataSet}]{\sphinxcrossref{BaseDataSet}}}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{batch\_size}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{int}}\sphinxparamcomma \sphinxparam{\DUrole{n}{shuffle}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{bool}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{True}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Bases: \sphinxcode{\sphinxupquote{object}}
\index{on\_epoch\_end() (m2aia.Generators.BatchGenerator method)@\spxentry{on\_epoch\_end()}\spxextra{m2aia.Generators.BatchGenerator method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Generators.BatchGenerator.on_epoch_end}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{on\_epoch\_end}}}{}{}
\pysigstopsignatures
\end{fulllineitems}


\end{fulllineitems}

\end{quote}


\chapter{m2aia.ImageIO module}
\label{\detokenize{index:module-m2aia.ImageIO}}\label{\detokenize{index:m2aia-imageio-module}}\index{module@\spxentry{module}!m2aia.ImageIO@\spxentry{m2aia.ImageIO}}\index{m2aia.ImageIO@\spxentry{m2aia.ImageIO}!module@\spxentry{module}}\index{ImzMLReader (class in m2aia.ImageIO)@\spxentry{ImzMLReader}\spxextra{class in m2aia.ImageIO}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader}}
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\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{class\DUrole{w}{ }}}\sphinxcode{\sphinxupquote{m2aia.ImageIO.}}\sphinxbfcode{\sphinxupquote{ImzMLReader}}}{\sphinxparam{\DUrole{n}{imzML\_path}}\sphinxparamcomma \sphinxparam{\DUrole{n}{baseline\_correction}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}TopHat\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Median\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{\textquotesingle{}None\textquotesingle{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{baseline\_correction\_half\_window\_size}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{int}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{50}}\sphinxparamcomma \sphinxparam{\DUrole{n}{normalization}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}TIC\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Sum\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Mean\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Max\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}RMS\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Internal\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}External\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{\textquotesingle{}None\textquotesingle{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{smoothing}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}SavitzkyGolay\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Gaussian\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{\textquotesingle{}None\textquotesingle{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{smoothing\_half\_window\_size}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{int}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{2}}\sphinxparamcomma \sphinxparam{\DUrole{n}{intensity\_transformation}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}Log2\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Log10\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}SquareRoot\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{\textquotesingle{}None\textquotesingle{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{pooling}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}Mean\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Median\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Maximum\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Sum\textquotesingle{}}\DUrole{p}{{]}}}\DUrole{w}{ }\DUrole{o}{=}\DUrole{w}{ }\DUrole{default_value}{\textquotesingle{}Maximum\textquotesingle{}}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Bases: \sphinxcode{\sphinxupquote{object}}

\sphinxAtStartPar
Wrapper class for M2aia’s imzML reader \sphinxurl{https://github.com/m2aia/m2aia}.

\sphinxAtStartPar
Complete processing examples with focus on deep learning can be found on \sphinxurl{https://github.com/m2aia/pym2aia-examples}

\sphinxAtStartPar
Example usage:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{k+kn}{import} \PYG{n+nn}{m2aia} \PYG{k}{as} \PYG{n+nn}{m2}

\PYG{n}{I} \PYG{o}{=} \PYG{n}{m2}\PYG{o}{.}\PYG{n}{ImzMLReader}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{path/to/imzMl/file.imzML}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{SetNormalization}\PYG{p}{(}\PYG{n}{m2}\PYG{o}{.}\PYG{n}{m2NormalizationTIC}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{SetIntensityTransformation}\PYG{p}{(}\PYG{n}{m2}\PYG{o}{.}\PYG{n}{m2IntensityTransformationSquareRoot}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{Execute}\PYG{p}{(}\PYG{p}{)}
\PYG{n}{ys\PYGZus{}2} \PYG{o}{=} \PYG{n}{I}\PYG{o}{.}\PYG{n}{GetMeanSpectrum}\PYG{p}{(}\PYG{p}{)}
\PYG{n}{i\PYGZus{}2} \PYG{o}{=} \PYG{n}{I}\PYG{o}{.}\PYG{n}{GetArray}\PYG{p}{(}\PYG{n}{imz}\PYG{p}{,} \PYG{l+m+mi}{75}\PYG{p}{)}
\end{sphinxVerbatim}
\index{CheckHandle() (m2aia.ImageIO.ImzMLReader method)@\spxentry{CheckHandle()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.CheckHandle}}
\pysigstartsignatures
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\pysigstopsignatures
\sphinxAtStartPar
Check if the handle was initialized properly.
To prevent this check from throwing an exception you must call Execute() once.
\begin{quote}\begin{description}
\sphinxlineitem{Raises}
\sphinxAtStartPar
ReferenceError: is invalid file name and or not yet called Execute().

\end{description}\end{quote}

\end{fulllineitems}

\index{GetArray() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetArray()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetArray}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetArray}}}{\sphinxparam{\DUrole{n}{center}}\sphinxparamcomma \sphinxparam{\DUrole{n}{tol}}\sphinxparamcomma \sphinxparam{\DUrole{n}{dtype=\textless{}class \textquotesingle{}numpy.float32\textquotesingle{}\textgreater{}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{squeeze: bool = False}}}{{ $\rightarrow$ ndarray}}
\pysigstopsignatures
\sphinxAtStartPar
Get the (ion) image data as numpy array.
The pixel values are the pooled intensities (ie. pooling strategies like
the ‘Mean’, ‘Median’, ‘Maximum’, or ‘Sum’) in the interval {[}center\sphinxhyphen{}tol, center+tol{]} of the spectra.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
Numpy array of size {[}x,y,z{]} with dtype=dtype.

\sphinxlineitem{Parameters}\begin{itemize}
\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{center}} \textendash{} value on the x axis.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{tol}} \textendash{} tolerance for query points on the x axis around the center.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{dtype}} \textendash{} array element type {[}np.float32, np.float64{]}.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{squeeze}} \textendash{} Remove all dimensions if any is smaller or equals 1.

\end{itemize}

\sphinxlineitem{Raises}
\sphinxAtStartPar
TypeError: Image pixel type is not one of {[}np.float32, np.float64{]}

\end{description}\end{quote}

\end{fulllineitems}

\index{GetImage() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetImage()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetImage}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetImage}}}{\sphinxparam{\DUrole{n}{center}}\sphinxparamcomma \sphinxparam{\DUrole{n}{tol}}\sphinxparamcomma \sphinxparam{\DUrole{n}{dtype=\textless{}class \textquotesingle{}numpy.float32\textquotesingle{}\textgreater{}}}}{{ $\rightarrow$ Image}}
\pysigstopsignatures
\sphinxAtStartPar
Get the (ion) image data as parameterized SimpleITK.Image.

\sphinxAtStartPar
\sphinxcode{\sphinxupquote{m2aia.ImzMLReader.GetArray()}}
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
sitk.Image of size {[}x,y,z{]} with dtype=dtype.

\sphinxlineitem{Parameters}\begin{itemize}
\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{center}} \textendash{} value on the x axis.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{tol}} \textendash{} tolerance for query points on the x axis around the center.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{dtype}} \textendash{} array element type {[}np.float32, np.float64{]}.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{squeeze}} \textendash{} Remove all dimensions if any is smaller or equals 1.

\end{itemize}

\sphinxlineitem{Raises}
\sphinxAtStartPar
TypeError: Image pixel type is not one of {[}np.float32, np.float64{]}

\end{description}\end{quote}

\end{fulllineitems}

\index{GetIndexArray() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetIndexArray()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetIndexArray}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetIndexArray}}}{}{{ $\rightarrow$ ndarray}}
\pysigstopsignatures
\sphinxAtStartPar
Get the index image data as numpy array.
The pixel values are the spectrum IDs starting with 0. Use the mask array to identify valid spectrum IDs.

\sphinxAtStartPar
Access valid spectrum IDs:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n}{indexImage} \PYG{o}{=} \PYG{n}{I}\PYG{o}{.}\PYG{n}{GetIndexArray}\PYG{p}{(}\PYG{p}{)}
\PYG{n}{maskImage} \PYG{o}{=} \PYG{n}{I}\PYG{o}{.}\PYG{n}{GetMaskArray}\PYG{p}{(}\PYG{p}{)}
\PYG{n}{validIndices} \PYG{o}{=} \PYG{n}{indexImage}\PYG{p}{[}\PYG{n}{maskImage} \PYG{o}{\PYGZgt{}} \PYG{l+m+mi}{0}\PYG{p}{]}
\end{sphinxVerbatim}
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
Numpy array of size {[}x,y,z{]} with dtype=np.uint32.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetIndexImage() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetIndexImage()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetIndexImage}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetIndexImage}}}{}{}
\pysigstopsignatures\begin{description}
\sphinxlineitem{Get the index image data as parameterized SimpleITK.Image.}
\sphinxAtStartPar
This method calls \sphinxcode{\sphinxupquote{GetIndexArray()}}

\end{description}
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
sitk.Image of size {[}x,y,z{]} with dtype=np.uint32.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetIntensities() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetIntensities()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetIntensities}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetIntensities}}}{\sphinxparam{\DUrole{n}{index}}\sphinxparamcomma \sphinxparam{\DUrole{n}{ys}\DUrole{o}{=}\DUrole{default_value}{None}}}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Query the y\sphinxhyphen{}axis (ys) values for a given spectrum id.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}\begin{itemize}
\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{index}} \textendash{} Id of a spectrum in the image.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{ys}} \textendash{} By passing a np.array (dtype=np.float32) from external, this np.array can
be reused and do not require an extra memory allocation. Otherwise
a new array is created.

\end{itemize}

\sphinxlineitem{Returns}
\sphinxAtStartPar
A list of two np.array elements {[}xs,ys{]}. xs = x\sphinxhyphen{}values; ys = y\sphinxhyphen{}values.

\sphinxlineitem{Raises}
\sphinxAtStartPar
IndexError: if index is not in the range of valid spectra indices {[}0,self.number\_of\_spectra\sphinxhyphen{}1{]}.
TypeError: if the ImzML file format is not continuous profile/centroid!

\end{description}\end{quote}

\end{fulllineitems}

\index{GetMaskArray() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetMaskArray()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetMaskArray}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetMaskArray}}}{}{{ $\rightarrow$ ndarray}}
\pysigstopsignatures
\sphinxAtStartPar
Get the mask image data as numpy array.
The binary mask indicates valid spectra (pixel value \textgreater{}= 1) and background (pixel value == 0).
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
Numpy array of size {[}x,y,z{]} with dtype=np.ushort.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetMaskImage() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetMaskImage()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetMaskImage}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetMaskImage}}}{}{{ $\rightarrow$ Image}}
\pysigstopsignatures
\sphinxAtStartPar
Get the mask image data as parameterized SimpleITK.Image.
The pixel values indicate valid spectra (pixel value \textgreater{}= 1) and background (pixel value == 0).
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
sitk.Image of size {[}x,y,z{]} with dtype=np.ushort.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetMaxSpectrum() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetMaxSpectrum()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetMaxSpectrum}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetMaxSpectrum}}}{}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the overview spectrum (max over all spectra).
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
np.array with maximum intensity values of all spectra.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetMeanSpectrum() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetMeanSpectrum()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetMeanSpectrum}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetMeanSpectrum}}}{}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the overview spectrum (mean over all spectra).
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
np.array with mean intensity values of all spectra.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetMetaData() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetMetaData()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetMetaData}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetMetaData}}}{}{{ $\rightarrow$ Dict\DUrole{p}{{[}}str\DUrole{p}{,}\DUrole{w}{ }str\DUrole{p}{{]}}}}
\pysigstopsignatures
\sphinxAtStartPar
Returns a dictionary of all meta data information retrieved by m2aia.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
List of strings of meta data.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetNormalizationArray() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetNormalizationArray()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetNormalizationArray}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetNormalizationArray}}}{\sphinxparam{\DUrole{n}{type}}}{{ $\rightarrow$ ndarray}}
\pysigstopsignatures
\sphinxAtStartPar
Get a normalization image data as numpy array.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
Numpy array of size {[}x,y,z{]} with dtype=np.float64.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetNormalizationImage() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetNormalizationImage()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetNormalizationImage}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetNormalizationImage}}}{\sphinxparam{\DUrole{n}{type}}}{{ $\rightarrow$ Image}}
\pysigstopsignatures
\sphinxAtStartPar
Get a normalization image data as parameterized SimpleITK.Image.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
sitk.Image of size {[}x,y,z{]} with dtype=np.float64.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetNumberOfSpectra() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetNumberOfSpectra()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetNumberOfSpectra}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetNumberOfSpectra}}}{}{{ $\rightarrow$ int}}
\pysigstopsignatures
\sphinxAtStartPar
Get the number of valid spectra in the image.
This can be used to iterate over all spectra in the image using
a for loop:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{GetNumberOfSpectra}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
    \PYG{n}{xs}\PYG{p}{,} \PYG{n}{ys} \PYG{o}{=} \PYG{n}{reader}\PYG{o}{.}\PYG{n}{GetSpectrum}\PYG{p}{(}\PYG{n}{i}\PYG{p}{)}
\end{sphinxVerbatim}
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
Number of valid spectra.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetOrigin() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetOrigin()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetOrigin}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetOrigin}}}{}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the image origin.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
The origin in world coordinates of the image as numpy array of size {[}3{]} and dtype=np.float64.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetParametersAsFormattedString() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetParametersAsFormattedString()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetParametersAsFormattedString}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetParametersAsFormattedString}}}{}{}
\pysigstopsignatures
\sphinxAtStartPar
Transform signal processing parameters into a fomatted string representation.

\end{fulllineitems}

\index{GetShape() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetShape()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetShape}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetShape}}}{}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the shape of the image.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
numpy array of size {[}3{]} for the x,y,z image dimensions (in number of pixels).

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSizeInBytesOfYAxisType() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSizeInBytesOfYAxisType()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSizeInBytesOfYAxisType}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSizeInBytesOfYAxisType}}}{}{{ $\rightarrow$ int}}
\pysigstopsignatures
\sphinxAtStartPar
Get number of bytes used to store the intensity values.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
The number of bytes.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSpacing() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSpacing()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSpacing}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSpacing}}}{}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the pixel spacing of the image
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
numpy array of size {[}3{]} and dtype=np.float64 for the pixel size in x,y,z dimension (in millimeter).

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSpectra() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSpectra()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSpectra}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSpectra}}}{\sphinxparam{\DUrole{n}{indices}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List\DUrole{p}{{[}}int\DUrole{p}{{]}}}}}{{ $\rightarrow$ ndarray}}
\pysigstopsignatures
\sphinxAtStartPar
Query a set of intensities by a list of indices.
Only continuous imzML files.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{indices}} \textendash{} List of Ids of spectra in the image.

\sphinxlineitem{Returns}
\sphinxAtStartPar
a np.ndarray of shape {[}len(indices), self.depth{]}.

\sphinxlineitem{Raises}
\sphinxAtStartPar
IndexError: if index is not in the range of valid spectra indices {[}0,self.number\_of\_spectra\sphinxhyphen{}1{]}.
TypeError: if the ImzML file format is not continuous profile/centroid!

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSpectrum() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSpectrum()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSpectrum}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSpectrum}}}{\sphinxparam{\DUrole{n}{index}}}{{ $\rightarrow$ List\DUrole{p}{{[}}array\DUrole{p}{{]}}}}
\pysigstopsignatures
\sphinxAtStartPar
Query the x\sphinxhyphen{}axis (xs) and y\sphinxhyphen{}axis (ys) values for a given spectrum id.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{index}} \textendash{} Id of a spectrum in the image.

\sphinxlineitem{Returns}
\sphinxAtStartPar
A list of two np.array elements {[}xs,ys{]}. xs = x\sphinxhyphen{}values; ys = y\sphinxhyphen{}values.

\sphinxlineitem{Raises}
\sphinxAtStartPar
IndexError: if index is not in the range of valid spectra indices {[}0,self.number\_of\_spectra\sphinxhyphen{}1{]}.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSpectrumDepth() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSpectrumDepth()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSpectrumDepth}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSpectrumDepth}}}{\sphinxparam{\DUrole{n}{id}}}{{ $\rightarrow$ int}}
\pysigstopsignatures
\sphinxAtStartPar
Get the size of the x axis for a specific spectrum of the image.
This method is helpful for processed (centroid) imzML files. For continuous
(centroid/profile) imzML files use GetXAxisDepth(self).
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{id}} \textendash{} Id of a spectrum in the image.

\sphinxlineitem{Returns}
\sphinxAtStartPar
Number of x values.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSpectrumPosition() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSpectrumPosition()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSpectrumPosition}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSpectrumPosition}}}{\sphinxparam{\DUrole{n}{id}}}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the image index position for a given spectrum id.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{id}} \textendash{} the id of a spectrum (may be different to the ids given in the imzML).

\sphinxlineitem{Returns}
\sphinxAtStartPar
Position in index coordinates as numpy array of size {[}3{]} and dtype=np.int32.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetSpectrumType() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetSpectrumType()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetSpectrumType}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetSpectrumType}}}{}{{ $\rightarrow$ str}}
\pysigstopsignatures
\sphinxAtStartPar
Get the imzML type, i.e. continuous/processed profile/centroid.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
The type of the imzML as string.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetTolerance() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetTolerance()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetTolerance}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetTolerance}}}{}{{ $\rightarrow$ float32}}
\pysigstopsignatures
\sphinxAtStartPar
Get the current tolerance value.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
np.float32
The current tolerance value.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetXAxis() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetXAxis()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetXAxis}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetXAxis}}}{}{{ $\rightarrow$ array}}
\pysigstopsignatures
\sphinxAtStartPar
Get the x axis values (i.e. m/z values on the x axis).
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
np.array

\end{description}\end{quote}

\end{fulllineitems}

\index{GetXAxisDepth() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetXAxisDepth()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetXAxisDepth}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetXAxisDepth}}}{}{{ $\rightarrow$ int}}
\pysigstopsignatures
\sphinxAtStartPar
Get the size of the x axis. For processed imzML files,
this value is the number of bins used to represent the x\sphinxhyphen{}axis.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
Number of x values.

\end{description}\end{quote}

\end{fulllineitems}

\index{GetYDataType() (m2aia.ImageIO.ImzMLReader method)@\spxentry{GetYDataType()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.GetYDataType}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{GetYDataType}}}{}{}
\pysigstopsignatures
\sphinxAtStartPar
Return the intensity data type defined in the imzML file.
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
np.float32 or np.float64; if not defined return None

\end{description}\end{quote}

\end{fulllineitems}

\index{Load() (m2aia.ImageIO.ImzMLReader method)@\spxentry{Load()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.Load}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{Load}}}{}{}
\pysigstopsignatures
\end{fulllineitems}

\index{SetBaselineCorrection() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SetBaselineCorrection()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SetBaselineCorrection}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SetBaselineCorrection}}}{\sphinxparam{\DUrole{n}{strategy}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}TopHat\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Median\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{half\_window\_size}\DUrole{o}{=}\DUrole{default_value}{50}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Set the baseline correction strategy.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}\begin{itemize}
\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{strategy}} \textendash{} Set the basline correction strategy using one of the m2BaselineCorrection literals.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{half\_window\_size}} \textendash{} 2*half\_window\_size + 1 spectrum points are used for BaselineCorrection.

\end{itemize}

\end{description}\end{quote}

\end{fulllineitems}

\index{SetIntensityTransformation() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SetIntensityTransformation()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SetIntensityTransformation}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SetIntensityTransformation}}}{\sphinxparam{\DUrole{n}{strategy}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}Log2\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Log10\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}SquareRoot\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Set the intensity transformation strategy.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{strategy}} \textendash{} m2IntensityTransformation
Set the intensity transformation strategy using one of the m2IntensityTransformation literals.

\end{description}\end{quote}

\end{fulllineitems}

\index{SetNormalization() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SetNormalization()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SetNormalization}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SetNormalization}}}{\sphinxparam{\DUrole{n}{strategy}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}TIC\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Sum\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Mean\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Max\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}RMS\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Internal\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}External\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Set the normalization strategy.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{strategy}} \textendash{} m2Normalization
Set the normalization strategy using one of the m2Normalization literals.

\end{description}\end{quote}

\end{fulllineitems}

\index{SetPooling() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SetPooling()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SetPooling}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SetPooling}}}{\sphinxparam{\DUrole{n}{strategy}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}Mean\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Median\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Maximum\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Sum\textquotesingle{}}\DUrole{p}{{]}}}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Set the pooling strategy.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{strategy}} \textendash{} m2Pooling
Set the pooling strategy using one of the m2Pooling literals.

\end{description}\end{quote}

\end{fulllineitems}

\index{SetSmoothing() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SetSmoothing()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SetSmoothing}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SetSmoothing}}}{\sphinxparam{\DUrole{n}{strategy}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Literal\DUrole{p}{{[}}\DUrole{s}{\textquotesingle{}SavitzkyGolay\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}Gaussian\textquotesingle{}}\DUrole{p}{,}\DUrole{w}{ }\DUrole{s}{\textquotesingle{}None\textquotesingle{}}\DUrole{p}{{]}}}}\sphinxparamcomma \sphinxparam{\DUrole{n}{half\_window\_size}\DUrole{o}{=}\DUrole{default_value}{2}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Set the spectrum smoothing strategy.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}\begin{itemize}
\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{strategy}} \textendash{} Set the smoothing strategy using one of the m2Smoothing literals.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{half\_window\_size}} \textendash{} 2*half\_window\_size + 1 spectrum points used for smoothing.

\end{itemize}

\end{description}\end{quote}

\end{fulllineitems}

\index{SetTolerance() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SetTolerance()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SetTolerance}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SetTolerance}}}{\sphinxparam{\DUrole{n}{tol}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{float32}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Set the tolerance value.
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{tol}} \textendash{} np.float32
The tolerance value to be set.

\end{description}\end{quote}

\end{fulllineitems}

\index{SpectrumIterator() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SpectrumIterator()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SpectrumIterator}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SpectrumIterator}}}{}{}
\pysigstopsignatures
\sphinxAtStartPar
Create a spectrum iterator/generator, yielding all valid spectra.
This can be used to iterate over all spectra in the image using
a for loop:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{k}{for} \PYG{n}{i}\PYG{p}{,}\PYG{n}{xs}\PYG{p}{,}\PYG{n}{ys} \PYG{o+ow}{in} \PYG{n}{reader}\PYG{o}{.}\PYG{n}{SpectrumIterator}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
    \PYG{o}{.}\PYG{o}{.}\PYG{o}{.}
\end{sphinxVerbatim}
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
a triplet with (i=spectrum\sphinxhyphen{}id, xs=x\sphinxhyphen{}values, ys=y\sphinxhyphen{}values)

\end{description}\end{quote}

\end{fulllineitems}

\index{SpectrumRandomBatchIterator() (m2aia.ImageIO.ImzMLReader method)@\spxentry{SpectrumRandomBatchIterator()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.SpectrumRandomBatchIterator}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{SpectrumRandomBatchIterator}}}{\sphinxparam{\DUrole{n}{batch\_size}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Create a spectrum batch iterator/generator, yielding a batch of ys\sphinxhyphen{}values of spectra in a random order with repetitions.

\sphinxAtStartPar
Example:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{k}{for} \PYG{n}{ys\PYGZus{}batch} \PYG{o+ow}{in} \PYG{n}{reader}\PYG{o}{.}\PYG{n}{SpectrumRandomBatchIterator}\PYG{p}{(}\PYG{n}{batch\PYGZus{}size} \PYG{o}{=} \PYG{n}{N}\PYG{p}{)}\PYG{p}{:}
    \PYG{o}{.}\PYG{o}{.}\PYG{o}{.}
\end{sphinxVerbatim}
\begin{quote}\begin{description}
\sphinxlineitem{Returns}
\sphinxAtStartPar
a np.array as batch of intensities with shape {[}batch\_size, self.depth{]}

\end{description}\end{quote}

\end{fulllineitems}

\index{WriteContinuousCentroidImzML() (m2aia.ImageIO.ImzMLReader method)@\spxentry{WriteContinuousCentroidImzML()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.WriteContinuousCentroidImzML}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{WriteContinuousCentroidImzML}}}{\sphinxparam{\DUrole{n}{path}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{str}}\sphinxparamcomma \sphinxparam{\DUrole{n}{centroids}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Given a list of centroids, write a continuous centroid imzML to the given path.
Use ‘SetTolerance’ to define the range query for each centroid (ppm).
\begin{quote}\begin{description}
\sphinxlineitem{Parameters}\begin{itemize}
\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{path}} \textendash{} Target file path the \textless{}path\textgreater{}.imzML and the \textless{}path\textgreater{}.ibd is written to.

\item {} 
\sphinxAtStartPar
\sphinxstyleliteralstrong{\sphinxupquote{centroids}} \textendash{} a list of centroids.

\end{itemize}

\end{description}\end{quote}

\sphinxAtStartPar
Example usage:

\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{k+kn}{import} \PYG{n+nn}{m2aia} \PYG{k}{as} \PYG{n+nn}{m2}

\PYG{n}{I} \PYG{o}{=} \PYG{n}{m2}\PYG{o}{.}\PYG{n}{ImzMLReader}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{path/to/imzMl/file.imzML}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{Execute}\PYG{p}{(}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{SetTolerance}\PYG{p}{(}\PYG{l+m+mi}{75}\PYG{p}{)}
\PYG{n}{I}\PYG{o}{.}\PYG{n}{WriteContinuousCentroidImzML}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{path/to/imzMl/file.imzML}\PYG{l+s+s2}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{300}\PYG{p}{,} \PYG{l+m+mi}{400}\PYG{p}{,} \PYG{l+m+mi}{500}\PYG{p}{]}\PYG{p}{)}
\end{sphinxVerbatim}

\end{fulllineitems}

\index{dir() (m2aia.ImageIO.ImzMLReader method)@\spxentry{dir()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.dir}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{dir}}}{}{{ $\rightarrow$ Path}}
\pysigstopsignatures
\sphinxAtStartPar
Absolute path to directory containing the referenced imzML

\end{fulllineitems}

\index{name() (m2aia.ImageIO.ImzMLReader method)@\spxentry{name()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.name}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{name}}}{}{{ $\rightarrow$ str}}
\pysigstopsignatures
\sphinxAtStartPar
Name (including file ending) of the given imzML

\end{fulllineitems}

\index{path() (m2aia.ImageIO.ImzMLReader method)@\spxentry{path()}\spxextra{m2aia.ImageIO.ImzMLReader method}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.ImageIO.ImzMLReader.path}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxbfcode{\sphinxupquote{path}}}{}{{ $\rightarrow$ Path}}
\pysigstopsignatures
\sphinxAtStartPar
Absolute path to the referenced imzML

\end{fulllineitems}


\end{fulllineitems}



\chapter{m2aia.Library module}
\label{\detokenize{index:module-m2aia.Library}}\label{\detokenize{index:m2aia-library-module}}\index{module@\spxentry{module}!m2aia.Library@\spxentry{m2aia.Library}}\index{m2aia.Library@\spxentry{m2aia.Library}!module@\spxentry{module}}\index{get\_library() (in module m2aia.Library)@\spxentry{get\_library()}\spxextra{in module m2aia.Library}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Library.get_library}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxcode{\sphinxupquote{m2aia.Library.}}\sphinxbfcode{\sphinxupquote{get\_library}}}{}{}
\pysigstopsignatures
\end{fulllineitems}

\index{get\_shared\_lib\_dependencies() (in module m2aia.Library)@\spxentry{get\_shared\_lib\_dependencies()}\spxextra{in module m2aia.Library}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Library.get_shared_lib_dependencies}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxcode{\sphinxupquote{m2aia.Library.}}\sphinxbfcode{\sphinxupquote{get\_shared\_lib\_dependencies}}}{\sphinxparam{\DUrole{n}{so\_file\_path}}}{}
\pysigstopsignatures
\end{fulllineitems}

\index{load\_library\_dependencies\_recursively() (in module m2aia.Library)@\spxentry{load\_library\_dependencies\_recursively()}\spxextra{in module m2aia.Library}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Library.load_library_dependencies_recursively}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxcode{\sphinxupquote{m2aia.Library.}}\sphinxbfcode{\sphinxupquote{load\_library\_dependencies\_recursively}}}{\sphinxparam{\DUrole{n}{search\_path}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{Path}}\sphinxparamcomma \sphinxparam{\DUrole{n}{library\_name}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{str}}\sphinxparamcomma \sphinxparam{\DUrole{n}{dependencies}\DUrole{p}{:}\DUrole{w}{ }\DUrole{n}{List}}}{}
\pysigstopsignatures
\sphinxAtStartPar
Load required M2aia libraries recursively

\end{fulllineitems}

\index{load\_m2aia\_library() (in module m2aia.Library)@\spxentry{load\_m2aia\_library()}\spxextra{in module m2aia.Library}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.Library.load_m2aia_library}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxcode{\sphinxupquote{m2aia.Library.}}\sphinxbfcode{\sphinxupquote{load\_m2aia\_library}}}{}{}
\pysigstopsignatures
\end{fulllineitems}



\chapter{Module contents}
\label{\detokenize{index:module-m2aia}}\label{\detokenize{index:module-contents}}\index{module@\spxentry{module}!m2aia@\spxentry{m2aia}}\index{m2aia@\spxentry{m2aia}!module@\spxentry{module}}\index{prepare\_environment() (in module m2aia)@\spxentry{prepare\_environment()}\spxextra{in module m2aia}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.prepare_environment}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxcode{\sphinxupquote{m2aia.}}\sphinxbfcode{\sphinxupquote{prepare\_environment}}}{}{}
\pysigstopsignatures
\end{fulllineitems}

\index{validate\_environment() (in module m2aia)@\spxentry{validate\_environment()}\spxextra{in module m2aia}}

\begin{fulllineitems}
\phantomsection\label{\detokenize{index:m2aia.validate_environment}}
\pysigstartsignatures
\pysiglinewithargsret{\sphinxcode{\sphinxupquote{m2aia.}}\sphinxbfcode{\sphinxupquote{validate\_environment}}}{}{}
\pysigstopsignatures
\end{fulllineitems}



\renewcommand{\indexname}{Python Module Index}
\begin{sphinxtheindex}
\let\bigletter\sphinxstyleindexlettergroup
\bigletter{m}
\item\relax\sphinxstyleindexentry{m2aia}\sphinxstyleindexpageref{index:\detokenize{module-m2aia}}
\item\relax\sphinxstyleindexentry{m2aia.Dataset}\sphinxstyleindexpageref{index:\detokenize{module-m2aia.Dataset}}
\item\relax\sphinxstyleindexentry{m2aia.Generators}\sphinxstyleindexpageref{index:\detokenize{module-m2aia.Generators}}
\item\relax\sphinxstyleindexentry{m2aia.ImageIO}\sphinxstyleindexpageref{index:\detokenize{module-m2aia.ImageIO}}
\item\relax\sphinxstyleindexentry{m2aia.Library}\sphinxstyleindexpageref{index:\detokenize{module-m2aia.Library}}
\end{sphinxtheindex}

\renewcommand{\indexname}{Index}
\printindex
\end{document}