cuisto.compute

compute module, part of cuisto.

Contains actual computation functions.

get_distribution(df, col, hue, hue_filter, per_commonnorm, binlim, nbins=100)

Computes distribution of objects.

A global distribution using only col is computed, then it computes a distribution distinguishing values in the hue column. For the latter, it is possible to use a subset of the data ony, based on another column using hue_filter. This another column is determined with hue, if the latter is "hemisphere", then hue_filter is used in the "channel" color and vice-versa. per_commonnorm controls how they are normalized, either as a whole (True) or independantly (False).

Use cases : (1) single-channel, two hemispheres : col=x, hue=hemisphere, hue_filter="", per_commonorm=True. Computes a distribution for each hemisphere, the sum of the area of both is equal to 1. (2) three-channels, one hemisphere : col=x, hue=channel, hue_filter="Ipsi.", per_commonnorm=False. Computes a distribution for each channel only for points in the ipsilateral hemisphere. Each curve will have an area of 1.

Parameters:

Name	Type	Description	Default
df	DataFrame		required
col	str	Key in df, used to compute the distributions.	required
hue	str	Key in df. Criterion for additional distributions.	required
hue_filter	str	Further filtering for "per" distribution. - hue = channel : value is the name of one of the hemisphere - hue = hemisphere : value can be the name of a channel, a list of such or "all"	required
per_commonnorm	bool	Use common normalization for all hues (per argument).	required
binlim	list or tuple	First bin left edge and last bin right edge.	required
nbins	int	Number of bins. Default is 100.	100

Returns:

Name	Type	Description
df_distribution	DataFrame	DataFrame with bins, distribution, count and their per-hemisphere or per-channel variants.

Source code in cuisto/compute.py

def get_distribution(
    df: pd.DataFrame,
    col: str,
    hue: str,
    hue_filter: dict,
    per_commonnorm: bool,
    binlim: tuple | list,
    nbins=100,
) -> pd.DataFrame:
    """
    Computes distribution of objects.

    A global distribution using only `col` is computed, then it computes a distribution
    distinguishing values in the `hue` column. For the latter, it is possible to use a
    subset of the data ony, based on another column using `hue_filter`. This another
    column is determined with `hue`, if the latter is "hemisphere", then `hue_filter` is
    used in the "channel" color and vice-versa.
    `per_commonnorm` controls how they are normalized, either as a whole (True) or
    independantly (False).

    Use cases :
    (1) single-channel, two hemispheres : `col=x`, `hue=hemisphere`, `hue_filter=""`,
    `per_commonorm=True`. Computes a distribution for each hemisphere, the sum of the
    area of both is equal to 1.
    (2) three-channels, one hemisphere : `col=x`, hue=`channel`,
    `hue_filter="Ipsi.", per_commonnorm=False`. Computes a distribution for each channel
    only for points in the ipsilateral hemisphere. Each curve will have an area of 1.

    Parameters
    ----------
    df : pandas.DataFrame
    col : str
        Key in `df`, used to compute the distributions.
    hue : str
        Key in `df`. Criterion for additional distributions.
    hue_filter : str
        Further filtering for "per" distribution.
        - hue = channel : value is the name of one of the hemisphere
        - hue = hemisphere : value can be the name of a channel, a list of such or "all"
    per_commonnorm : bool
        Use common normalization for all hues (per argument).
    binlim : list or tuple
        First bin left edge and last bin right edge.
    nbins : int, optional
        Number of bins. Default is 100.

    Returns
    -------
    df_distribution : pandas.DataFrame
        DataFrame with `bins`, `distribution`, `count` and their per-hemisphere or
        per-channel variants.

    """

    # - Preparation
    bin_edges = np.linspace(*binlim, nbins + 1)  # create bins
    df_distribution = []  # prepare list of distributions

    # - Both hemispheres, all channels
    # get raw count per bins (histogram)
    count, bin_edges = np.histogram(df[col], bin_edges)
    # get normalized count (pdf)
    distribution, _ = np.histogram(df[col], bin_edges, density=True)
    # get bin centers rather than edges to plot them
    bin_centers = bin_edges[:-1] + np.diff(bin_edges) / 2

    # make a DataFrame out of that
    df_distribution.append(
        pd.DataFrame(
            {
                "bins": bin_centers,
                "distribution": distribution,
                "count": count,
                "hemisphere": "both",
                "channel": "all",
                "axis": col,  # keep track of what col. was used
            }
        )
    )

    # - Per additional criterion
    # select data
    df_sub = select_hemisphere_channel(df, hue, hue_filter, False)
    hue_values = df[hue].unique()  # get grouping values
    # total number of datapoints in the subset used for additional distribution
    length_total = len(df_sub)

    for value in hue_values:
        # select part and coordinates
        df_part = df_sub.loc[df_sub[hue] == value, col]

        # get raw count per bins (histogram)
        count, bin_edges = np.histogram(df_part, bin_edges)
        # get normalized count (pdf)
        distribution, _ = np.histogram(df_part, bin_edges, density=True)

        if per_commonnorm:
            # re-normalize so that the sum of areas of all sub-parts is 1
            length_part = len(df_part)  # number of datapoints in that hemisphere
            distribution *= length_part / length_total

        # get bin centers rather than edges to plot them
        bin_centers = bin_edges[:-1] + np.diff(bin_edges) / 2

        # make a DataFrame out of that
        df_distribution.append(
            pd.DataFrame(
                {
                    "bins": bin_centers,
                    "distribution": distribution,
                    "count": count,
                    hue: value,
                    "channel" if hue == "hemisphere" else "hemisphere": hue_filter,
                    "axis": col,  # keep track of what col. was used
                }
            )
        )

    return pd.concat(df_distribution)

get_regions_metrics(df_annotations, object_type, channel_names, meas_base_name, metrics_names)

Get a new DataFrame with cumulated axons segments length in each brain regions.

This is the quantification per brain regions for fibers-like objects, eg. axons. The returned DataFrame has columns "cum. length µm", "cum. length mm", "density µm^-1", "density mm^-1", "coverage index".

Parameters:

Name	Type	Description	Default
df_annotations	DataFrame	DataFrame with an entry for each brain regions, with columns "Area µm^2", "Name", "hemisphere", and "{object_type: channel} Length µm".	required
object_type	str	Object type (primary classification).	required
channel_names	dict	Map between original channel names to something else.	required
meas_base_name	str		required
metrics_names	dict		required

Returns:

Name	Type	Description
df_regions	DataFrame	DataFrame with brain regions name, area and metrics.

Source code in cuisto/compute.py

def get_regions_metrics(
    df_annotations: pd.DataFrame,
    object_type: str,
    channel_names: dict,
    meas_base_name: str,
    metrics_names: dict,
) -> pd.DataFrame:
    """
    Get a new DataFrame with cumulated axons segments length in each brain regions.

    This is the quantification per brain regions for fibers-like objects, eg. axons. The
    returned DataFrame has columns "cum. length µm", "cum. length mm", "density µm^-1",
    "density mm^-1", "coverage index".

    Parameters
    ----------
    df_annotations : pandas.DataFrame
        DataFrame with an entry for each brain regions, with columns "Area µm^2",
        "Name", "hemisphere", and "{object_type: channel} Length µm".
    object_type : str
        Object type (primary classification).
    channel_names : dict
        Map between original channel names to something else.
    meas_base_name : str
    metrics_names : dict

    Returns
    -------
    df_regions : pandas.DataFrame
        DataFrame with brain regions name, area and metrics.

    """
    # get columns names
    cols = df_annotations.columns
    # get columns with fibers lengths
    cols_colors = cols[
        cols.str.startswith(object_type) & cols.str.endswith(meas_base_name)
    ]
    # select relevant data
    cols_to_select = pd.Index(["Name", "hemisphere", "Area µm^2"]).append(cols_colors)
    # sum lengths and areas of each brain regions
    df_regions = (
        df_annotations[cols_to_select]
        .groupby(["Name", "hemisphere"])
        .sum()
        .reset_index()
    )

    # get measurement for both hemispheres (sum)
    df_both = df_annotations[cols_to_select].groupby(["Name"]).sum().reset_index()
    df_both["hemisphere"] = "both"
    df_regions = (
        pd.concat([df_regions, df_both], ignore_index=True)
        .sort_values(by="Name")
        .reset_index()
        .drop(columns="index")
    )

    # rename measurement columns to lower case
    df_regions = df_regions.rename(
        columns={
            k: k.replace(meas_base_name, meas_base_name.lower()) for k in cols_colors
        }
    )

    # update names
    meas_base_name = meas_base_name.lower()
    cols = df_regions.columns
    cols_colors = cols[
        cols.str.startswith(object_type) & cols.str.endswith(meas_base_name)
    ]

    # convert area in mm^2
    df_regions["Area mm^2"] = df_regions["Area µm^2"] / 1e6

    # prepare metrics
    if "µm" in meas_base_name:
        # fibers : convert to mm
        cols_to_convert = pd.Index([col for col in cols_colors if "µm" in col])
        df_regions[cols_to_convert.str.replace("µm", "mm")] = (
            df_regions[cols_to_convert] / 1000
        )
        metrics = [meas_base_name, meas_base_name.replace("µm", "mm")]
    else:
        # objects : count
        metrics = [meas_base_name]

    # density = measurement / area
    metric = metrics_names["density µm^-2"]
    df_regions[cols_colors.str.replace(meas_base_name, metric)] = df_regions[
        cols_colors
    ].divide(df_regions["Area µm^2"], axis=0)
    metrics.append(metric)
    metric = metrics_names["density mm^-2"]
    df_regions[cols_colors.str.replace(meas_base_name, metric)] = df_regions[
        cols_colors
    ].divide(df_regions["Area mm^2"], axis=0)
    metrics.append(metric)

    # coverage index = measurement² / area
    metric = metrics_names["coverage index"]
    df_regions[cols_colors.str.replace(meas_base_name, metric)] = (
        df_regions[cols_colors].pow(2).divide(df_regions["Area µm^2"], axis=0)
    )
    metrics.append(metric)

    # prepare relative metrics columns
    metric = metrics_names["relative measurement"]
    cols_rel_meas = cols_colors.str.replace(meas_base_name, metric)
    df_regions[cols_rel_meas] = np.nan
    metrics.append(metric)
    metric = metrics_names["relative density"]
    cols_dens = cols_colors.str.replace(meas_base_name, metrics_names["density mm^-2"])
    cols_rel_dens = cols_colors.str.replace(meas_base_name, metric)
    df_regions[cols_rel_dens] = np.nan
    metrics.append(metric)
    # relative metrics should be defined within each hemispheres (left, right, both)
    for hemisphere in df_regions["hemisphere"].unique():
        row_indexer = df_regions["hemisphere"] == hemisphere

        # relative measurement = measurement / total measurement
        df_regions.loc[row_indexer, cols_rel_meas] = (
            df_regions.loc[row_indexer, cols_colors]
            .divide(df_regions.loc[row_indexer, cols_colors].sum())
            .to_numpy()
        )

        # relative density = density / total density
        df_regions.loc[row_indexer, cols_rel_dens] = (
            df_regions.loc[
                row_indexer,
                cols_dens,
            ]
            .divide(df_regions.loc[row_indexer, cols_dens].sum())
            .to_numpy()
        )

    # collect channel names
    channels = (
        cols_colors.str.replace(object_type + ": ", "")
        .str.replace(" " + meas_base_name, "")
        .values.tolist()
    )
    # collect measurements columns names
    cols_metrics = df_regions.columns.difference(
        pd.Index(["Name", "hemisphere", "Area µm^2", "Area mm^2"])
    )
    for metric in metrics:
        cols_to_cat = [f"{object_type}: {cn} {metric}" for cn in channels]
        # make sure it's part of available metrics
        if not set(cols_to_cat) <= set(cols_metrics):
            raise ValueError(f"{cols_to_cat} not in DataFrame.")
        # group all colors in the same colors
        df_regions[metric] = df_regions[cols_to_cat].values.tolist()
        # remove original data
        df_regions = df_regions.drop(columns=cols_to_cat)

    # add a color tag, given their names in the configuration file
    df_regions["channel"] = len(df_regions) * [[channel_names[k] for k in channels]]
    metrics.append("channel")

    # explode the dataframe so that each color has an entry
    df_regions = df_regions.explode(metrics)

    return df_regions

normalize_starter_cells(df, cols, animal, info_file, channel_names)

Normalize data by the number of starter cells.

Parameters:

Name	Type	Description	Default
df	DataFrame	Contains the data to be normalized.	required
cols	list - like	Columns to divide by the number of starter cells.	required
animal	str	Animal ID to parse the number of starter cells.	required
info_file	str	Full path to the TOML file with informations.	required
channel_names	dict	Map between original channel names to something else.	required

Returns:

Type	Description
DataFrame	Same df with normalized count.

Source code in cuisto/compute.py

def normalize_starter_cells(
    df: pd.DataFrame, cols: list[str], animal: str, info_file: str, channel_names: dict
) -> pd.DataFrame:
    """
    Normalize data by the number of starter cells.

    Parameters
    ----------
    df : pd.DataFrame
        Contains the data to be normalized.
    cols : list-like
        Columns to divide by the number of starter cells.
    animal : str
        Animal ID to parse the number of starter cells.
    info_file : str
        Full path to the TOML file with informations.
    channel_names : dict
        Map between original channel names to something else.

    Returns
    -------
    pd.DataFrame
        Same `df` with normalized count.

    """
    for channel in df["channel"].unique():
        # inverse mapping channel colors : names
        reverse_channels = {v: k for k, v in channel_names.items()}
        nstarters = get_starter_cells(animal, reverse_channels[channel], info_file)

        for col in cols:
            df.loc[df["channel"] == channel, col] = (
                df.loc[df["channel"] == channel, col] / nstarters
            )

    return df