Submodules¶
spt.analytic_expressions¶
Some analytic expressions used in other submodules, e.g. fitting functions, cdf, …
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spt.analytic_expressions.
ecdf
(x)¶ Calculate experimental continuous distribution function (ECDF), i.e. no binning, of random variable x so that ECDF(value)=probability(x>=value). I.e first value of counts=1.
- Equivalent to inverse of:
matplotlib.pyplot.hist(tau_dist,bins=numpy.unique(tau_dist),normed=True,cumulative=True)
but with non-equidistant binning, but bins are chosen according to unique values in x.
Parameters: x (numpy.array) – 1 dimensional array of random variable Returns: - [0](numpy.array): Bins of ECDF corresponding to unique values of x.
- [1](numpy.array): ECDF(value)=probability(x>=value).
Return type: list
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spt.analytic_expressions.
exp_tracks_per_frame
(x, a, b)¶ Exponential like decay to fit number of tracks per frame:
NoTracks=a*np.exp(-x/b)+c
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spt.analytic_expressions.
gauss_1D
(x, x0, sigma, A)¶ Simple 1D non-normalized Gaussian function:
y=np.absolute(A)*np.exp(-(x-x0)**2/sigma**2)
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spt.analytic_expressions.
gauss_Ncomb
(x, p, N)¶ Sum of N 1D Gaussian functions, see gauss_1D(x,x0,sigma,A). The nth Gaussian function with
n in [0,N[
is:- centered at multiples of first Gaussian center
(n+1)*x0
- has a width of
sqrt(n+1)*sigma
assuming Poissonian broadening - but decoupled Amplitudes
An
Parameters: - x (np.array) – Values at which function is evaluated
- p (list) –
[x0,sigma,A0,A1,...,AN]
input parameters for sum of Gaussians (len=N+2) - N (integer) – Number of Gaussian functions that are summed up
Returns: Evaluation of function at
x
,p
,N
Return type: np.array
- centered at multiples of first Gaussian center
spt.analyze¶
Further evaluate (averaging, …) _tprops. or _tmobprops.hdf5 files, i.e. to generate end result of kinetic analysis.
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spt.analyze.
fit_Ncomb
(x, y, centers_init, N)¶
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spt.analyze.
fit_levels
(data, centers_init)¶
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spt.analyze.
fit_tracks_per_frame
(n_tracks)¶ Fit number of trajectories per frame with deaying exponential
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spt.analyze.
get_NgT
(df)¶ Return average and 25%/75% interquartile range of all NgT related values.
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spt.analyze.
get_T_with_N
(df)¶ Return critical times of NgT
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spt.analyze.
get_half_time
(df)¶ Get half life time, i.e. 1-ecdf (means bigger than T) of start times for different ignore values.
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spt.analyze.
get_mobile_props
(df_in, infos, px, CycleTime, remove_immob=True)¶
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spt.analyze.
get_props
(df)¶ - Wrapper function to combine:
- get_half_time(df)
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spt.analyze.
get_result
(df, name)¶
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spt.analyze.
tracks_per_frame
(props, NoFrames)¶ Count number of trajectories per frame.
spt.immobile_props¶
Kinetic properties of picks for immobilized samples, e.g. TPP, photons, binding events, …
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spt.immobile_props.
apply_props
(df, ignore=1)¶ Group _picked.hdf5 by groups (i.e. picks in picasso.addon) and apply get_props() to each group to get immobile properties as in spt.
Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon
- ignore (int=1) – Maximum interruption (frames) allowed to be regarded as one bright time.
Returns: Output of get_props() for each group in
df
(groupby-apply approach).Return type: pandas.DataFrame
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spt.immobile_props.
apply_props_dask
(df, ignore=1)¶ Same as apply_props() but in parallelized version using DASK by partitioning df. Local DASK cluster has to be started manually for efficient computation, see cluster_setup_howto().
Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon
- ignore (int=1) – Maximum interruption (frames) allowed to be regarded as one bright time.
Returns: Output of get_props() for each group in
df
(groupby-apply approach).Return type: pandas.DataFrame
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spt.immobile_props.
cluster_setup_howto
()¶ Print instruction howto start a DASK local cluster for efficient computation of apply_props_dask(). Fixed
scheduler_port=8787
is used to easily reconnect to cluster once it was started.
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spt.immobile_props.
filter_
(df, NoFrames, apply_filter=None)¶ Decide which filter to apply to the output of get_props(), either:
- ‘sd’ as given by filter_fix()
- ‘th’ as given by filter_nofix()
- ‘none’ if no filter should be applied
Parameters: - df (pandas.DataFrame) – Immobile properties as calulated by apply_props()
- NoFrames (int) – Length of measurement in frames of corresponding raw movie.
- apply_filter (str) – Either ‘sd’,’th’ or ‘none’. See above.
Returns: Positives in
df
according to chosen filter as described above.Return type: pandas.DataFrame
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spt.immobile_props.
filter_fix
(df)¶ Filter for immobilized single dye origami as described in spt. Positives are groups
- with a trajectory within the first 5 frames after the start of the measurement
- and number of trajectories within group lie in 90% interval of all groups
Parameters: df (pandas.DataFrame) – Immobile properties as calulated by apply_props() Returns: Positives in df
according to single dye filter as described above.Return type: pandas.DataFrame
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spt.immobile_props.
filter_nofix
(df, NoFrames)¶ Filter for immobilized origami with DNA-PAINT based tracking handle (TH) as described in spt. Positives are groups
- with a trajectory within the first 5 frames after the start of the measurement
- and number localizations within group are greater or equal to 20% of total measurement duration (in frames)
Parameters: df (pandas.DataFrame) – Immobile properties as calulated by apply_props() Returns: Positives in df
according to TH filter as described above.Return type: pandas.DataFrame
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spt.immobile_props.
get_NgT
(df, ignore=1)¶ Combine get_taubs() and tracks_greaterT() to return TPP as pd.Series for one group.
- Input equivalent to get_taubs().
- Output equivalent to tracks_greaterT()[0].
The function assumes that there is only one group in the localization list!
Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e._picked.hdf5 as in picasso.addon
- ignore (int=1) – Maximum interruption (frames) allowed to be regarded as one bright time.
Returns: Index consists of a combination of one of the following letters and T in frames.
- n: Number of tracks longer or equal to T, i.e. TPP as in spt
- s: Mean 1st frame of tracks longer or equal to T.
- p: Mean photons of tracks longer or equal to T.
- e: Mean relative standard deviation of photons of tracks longer or equal to T.
Return type: pandas.Series
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spt.immobile_props.
get_props
(df, ignore=1)¶ Combination of get_NgT(df,ignore) and get_start(df,ignore) and get_var(df).
Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon
- ignore (int=1) – Maximum interruption (frames) allowed to be regarded as one bright time.
Returns: Concatenated output of get_NgT(df,ignore) and get_start(df,ignore) and get_var(df).
Return type: pandas.Series
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spt.immobile_props.
get_start
(df, ignore)¶ For a list of
ignore
values, was there a bright time at the start of the measurement and of which duration? That means forignore=2
and the first bright time starting at frame=3 there was NO bright timeignore=3
and the first bright time starting at frame=3 there was a bright time of finite duration.
Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon
- ignore (list) – List of maximum interruption (frames) allowed to be regarded as one bright time.
Returns: Index has format
Tstart-i%i'%(ignore)
. The value is the duration of the bright time at start of measurement if it happened withinignore
.Return type: pandas.Series
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spt.immobile_props.
get_taubs
(df, ignore=1)¶ Get bright time distribution, i.e. the intervals of continuous localizations only interrupted by
ignore
for one group and additional properties of each bright time. I.e. a bright time corresponds to one trajectory in terms of single particle tracking. The function assumes that there is only one group in the localization list!Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e._picked.hdf5 as in picasso.addon
- ignore (int=1) – Maximum interruption (frames) allowed to be regarded as one bright time.
Returns: - [0](numpy.array): Bright times only interrupted by
ignore
- [1](numpy.array): 1st frame of each bright time
- [2](numpy.array): Mean photon values of each bright time
- [3](numpy.array): Relative standard deviation of photons of each bright time
Return type: list
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spt.immobile_props.
get_trace
(df, NoFrames, field='net_gradient')¶ Get continuous field vs. time trace of length=NoFrames for one group. The function assumes that there is only one group in the localization list!
Parameters: - df (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon
- NoFrames (int) – Length of measurement in frames of corresponding raw movie.
- field (str) – Column name in df, e.g. ‘photons’ for intensity vs. time trace.
Returns: Trace, e.g. continuous field vs. time trace of length=NoFrames for one group
Return type: numpy.array
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spt.immobile_props.
get_var
(df)¶ Get various properties for one group in _picked.hdf5 as in picasso.addon.
Parameters: df (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon Returns: Indices are means of all columns in df
plus …n_locs
: Number of localizationsphotons
: Not mean but median!std_photons
: Standard deviation of photons.bg
: Background photons. Not mean but median!sx
: Standard deviation of group inx
sy
: Standard deviation of group iny
min_frame
: Mimimum in framesmax_frame
: Maximum in frameslen
: max_frame-min_frame (see above)
Return type: pandas.Series
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spt.immobile_props.
main
(locs, info, path, **params)¶ Get immobile properties for each group in _picked.hdf5 file (see picasso.addon) and filter.
Parameters: - locs (pandas.DataFrame) – Grouped localization list, i.e. _picked.hdf5 as in picasso.addon
- info (list) – Info _picked.yaml to _picked.hdf5 localizations as list of dictionaries.
- path (str) – Path to _picked.hdf5 file.
Keyword Arguments: - ignore (int=1) – Maximum interruption (frames) allowed to be regarded as one bright time.
- parallel (bool=True) – Apply parallel computing using DASK? Local cluster should be started before according to cluster_setup_howto()
- filter (string='th') – Which filter to use, either None, ‘th’ or ‘sd’ or ‘none’
Returns: - [0](dict): Dict of keyword arguments passed to function.
- [1](pandas.DataFrame): Immobile properties of each group in
locs
as calulated by apply_props()
Return type: list
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spt.immobile_props.
tracks_greaterT
(track_length, track_start, track_photons, track_photons_std)¶ Get number of trajectories (bright times) per particle (group or pick) greater or equal to T, i.e. TPP in spt. The function takes returns of get_taubs() as input.
Parameters: - track_length (numpy.array) – Trajectory durations or bright times only interrupted by
ignore
. See get_taubs(). - track_start (numpy.array) – 1st frame of each trajectory. See get_taubs().
- track_photons (numpy.array) – Mean photon values of each bright time. See get_taubs().
- track_photons_std (numpy.array) – Relative standard deviation of photons of each bright time. See get_taubs().
Returns: [0](pandas.Series): Index consists of a combination of one of the following letters and T in frames.
- n: Number of tracks longer or equal to T, i.e. TPP as in spt
- s: Mean 1st frame of tracks longer or equal to T.
- p: Mean photons of tracks longer or equal to T.
- e: Mean relative standard deviation of photons of tracks longer or equal to T.
[1](numpy.array): T in frames
Return type: list
- track_length (numpy.array) – Trajectory durations or bright times only interrupted by
spt.linklocs¶
Linking of localizations into particle trajectories using trackpy.
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spt.linklocs.
drop_shorttracks
(df, min_n_locs=10)¶ Remove trajectories with less localizations than min_n_locs from output of get_link().
Parameters: - df (pandas.DataFrame) – Trajectories pandas.DataFrame, i.e. output of get_link() (see also trackpy.link())
- min_n_locs (int=10) – Trajectories having less localizations than min_n_locs will be removed from df
Returns: df
with short trajectories < min_n_locs removed.Return type: pandas.DataFrame
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spt.linklocs.
get_link
(locs, search_range, memory)¶ Apply trackpy.link_df() (trackpy) on localizations with given search_range and memory to get trajectories sorted by group and frame. All tracks shorter or equal to 10 frames are removed.
Parameters: - locs (pandas.DataFrame) – Localizations as generated by picasso.localize as pandas.DataFrame
- info (picasso.io) – Info _locs.yaml to _locs.hdf5 localizations as list of dictionaries.
- search_range (int) – Localizations within search_range (spatial) will be connected to tracks (see trackpy.link_df)
- memory (int) – Localizations within memory (temporal) will be connected to tracks (see trackpy.link_df)
Returns: Linked trajectories using trackpy.link().
group
instead ofparticle
column for picasso.render compatibility.- All trajectories with <= 10 localizations are already removed!!
Return type: pandas.DataFrame
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spt.linklocs.
main
(locs, info, path, **params)¶ Link localizations using trackpy.link_df() (trackpy) on localizations (picasso.localize) with given search_range and memory to get trajectories sorted by group and frame. All tracks shorter or equal to 10 frames are removed. Trajectories will be saved as
'_picked%i%i.hdf5'%(search_range,memory)
with corresponding info as .yaml.Parameters: - locs (pandas.DataFrame) – Localization list, i.e. _locs.hdf5 as in picasso.localize
- info (list) – Info _locs.yaml to _locs.hdf5 localizations as list of dictionaries.
- path (str) – Path to _locs.hdf5 file.
Keyword Arguments: - search_range (int) – Localizations within search_range (spatial) will be connected to tracks (see trackpy.link_df)
- memory (int) – Localizations within memory (temporal) will be connected to tracks (see trackpy.link_df)
Returns: - [0](dict): Dict of keyword arguments passed to function.
- [1](pandas.DataFrame): Trajectories by application of trackpy.link_df(). See above.
Return type: list
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spt.linklocs.
plot_scan_results
(df, prox)¶ Quickly plot results in scan_sr_mem().
Parameters: - df (pandas.DataFrame) – Return DataFrame of scan_sr_mem()[0].
- prox (float) – Return DataFrame of scan_sr_mem()[1].
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spt.linklocs.
scan_sr_mem
(locs, info, path, sr, mem, roi=True, timewindow=True)¶ Quick scan using get_link() (trackpy) algorithm using tuples of
search_ranges
andmemory
over center ROI and starting time window of the video. Corresponding plot will be saved using plot_scan_results(). This is implemented in order to quickly estimate optimum linking parameters.Parameters: - locs (pandas.DataFrame) – Localizations as generated by picasso.localize as pandas.DataFrame
- info (picasso.io) – Info _locs.yaml to _locs.hdf5 localizations as list of dictionaries.
- path (str) – Path to _locs.hdf5 file for saving output
- sr (list(int)) – List of search_ranges to scan (see trackpy.link)
- mem (list(int)) – List of memory values to scan (see trackpy.link)
- roi (bool=True) – If True scan is performed on cropped video to center 200^2 px FOV
- timewindow (bool=True) – If True scan is performed on first 300 frames of video only
Returns: [0] (pandas.DataFrame): Multi-Index: Tuple (
search_range
,memory
) with columns:len_med
: Median track lengthnumtracks
: Number of linked trackssearch_range
: See abovememory
: See above
[1] (float):
Proximity, i.e. 90% of all nearest neighbor distances between localizations corresponding to first 100 frames (full FOV) are greater than proximity (px).
Return type: list
spt.mob_props¶
Kinetic properties of trajectories for of mobile samples, e.g. MSD caluclation and fitting, …
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spt.mob_props.
apply_props
(df)¶ Group trajectories list (_pickedxxxx.hdf5) as obtained by linklocs.main() by groups (i.e. trajectories) and apply get_props() to each group to get mobile properties. See also spt.
Parameters: df (pandas.DataFrame) – Trajectories list (_pickedxxxx.hdf5) as obtained by linklocs.main() Returns: Output of get_props() for each group in df
(groupby-apply approach).Return type: pandas.DataFrame
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spt.mob_props.
apply_props_dask
(df)¶ Same as apply_props() but in parallelized version using DASK by partitioning df. Local DASK cluster has to be started manually for efficient computation, see cluster_setup_howto().
Parameters: df (pandas.DataFrame) – Trajectories list (_pickedxxxx.hdf5) as obtained by linklocs.main() Returns: Output of get_props() for each group in df
(groupby-apply approach).Return type: pandas.DataFrame
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spt.mob_props.
fit_msd_anomal
(lagtimes, msd)¶ Unweighted least square fit of invidual msd by anomalous model
msd=a*lagtimes**b
, see analytic_expressions.msd_anomal(). If there was less then two data-points or fit was not succesfull NaNs are returned as optimum parameters.Parameters: - lagtimes (np.array) – Array of msd lagtimes
- msd (np.array) – Mean square displacement (msd) at lagtimes
Returns: Column
a
corresponds to slope,b
corresponds to diffusion mode.Return type: pandas.Series
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spt.mob_props.
fit_msd_free
(lagtimes, msd, offset=False)¶ Unweighted least square fit of invidual msd by linear model
msd=a*lagtimes+b
, see analytic_expressions.msd_free(), i.e. assuming free Browninan motion. If there was less then two data-points or fit was not succesfull NaNs are returned as optimum parameters.Parameters: - lagtimes (np.array) – Array of msd lagtimes
- msd (np.array) – Mean square displacement (msd) at lagtimes
- offset (bool=False) – If True offset is used in linear fit model, if False
Returns: Column
a
corresponds to slope,b
corresponds to offset of linear function applied.Return type: pandas.Series
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spt.mob_props.
fit_msd_free_iterative
(lagtimes, msd, max_it=5)¶ Unweighted least square fit of invidual msd by linear model
msd=a*lagtimes+b
in iterative manner to find optimum fitting range of msd according to: Xavier Michalet, Physical Review E, 82, 2010 (michalet). In first iteration msd is fitted up to a maximum lagtime oflag_max=0.5*Nmsd
withNmsd
being the full msd length. Notice that motion_metrics.displacement_moments() calculates msd only up toNmsd=0.25*N
hencelag_max=0.125*N
with Nbeing the full lenght of the trajectory. Then fitting range is updated according to rulelag_max=int(np.round(2+2.3*(b/a)**0.52))
. For a detailed illustration please see SI of spt.Parameters: - lagtimes (np.array) – Array of msd lagtimes
- msd (np.array) – Mean square displacement (msd) at lagtimes
- max_it (int=5) – Maximum number of iterations
Returns: a
slope of linear function applied.b
offset of linear function appliedp
maximum lagtime up to which msd was fittedmax_it
resulting number of iterations until convergence was achieved
Return type: pandas.Series
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spt.mob_props.
get_props
(df)¶ Combination of immobile_props.get_var(df) and getfit_moments(df).
Parameters: df (pandas.DataFrame) – Trajectories (_pickedxxxx.hdf5) as obtained by linklocs.main() Returns: Concatenated output of immobile_props.get_var(df) and getfit_moments(df). Return type: pandas.Series
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spt.mob_props.
getfit_moments
(df)¶ Calculate msd of single trajectory using metrics.displacement_moments() and apply both linear iterative fitting according to fit_msd_free_iterative() and anomalous diffsuion model fitting using fit_msd_anomal() to msd.
Parameters: df (pandas.DataFrame) – Trajectories (_pickedxxxx.hdf5) as obtained by linklocs.main() Returns: Concatenated output of fit_msd_free_iterative() and fit_msd_anomal(). a_iter
slope of iterative linear fitb_iter
offset of iterative linear fitp_iter
maximum lagtime up to which msd was fitted for iterative linear fitmax_iter
resulting number of iterations until convergence was achieved for iterative linear fita
slope of anomalous fitb
diffusion mode of anomalous fit
Return type: pandas.Series
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spt.mob_props.
main
(locs, info, path, **params)¶ Get mobile properties for each group in trajectories list (_pickedxxxx.hdf5) file as obtained by linklocs.main().
Parameters: - locs (pandas.DataFrame) – Trajectories list (_pickedxxxx.hdf5) as obtained by linklocs.main()
- info (list) – Info _pickedxxxx.yaml to _pickedxxxx.hdf5 trajectories as list of dictionaries.
- path (str) – Path to _pickedxxxx.hdf5 file.
Keyword Arguments: parallel (bool=True) – Apply parallel computing using DASK? Local cluster should be started before according to cluster_setup_howto()
Returns: - [0](dict): Dict of keyword arguments passed to function.
- [1](pandas.DataFrame): Mobile properties of each group in
locs
as calulated by apply_props()
Return type: list
spt.motion_metrics¶
Numba optimized caluclation of motion metrics like MSD, MME, straightness, msd_ratio, …
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spt.motion_metrics.
displacement_moments
¶ Numba optimized calulation of trajectory
(t,x,y)
moments. Calulation accounts for short gaps, i.e. missed localizations recovered by allowedmemory
values. Moments are only calulated up to maximum lag time ofl_max = 0.25*N
withN=len(t)
. Calulated moments are:- Mean square displacement (MSD)
- Mean displacement moment of 4th order (MSD corresponds to 2nd order)
- Mean maximal excursion of 2nd order (MME)
- Mean maximal excursion of 4th order
MME is calculated according to: Vincent Tejedor, Biophysical Journal, 98, 7, 2010 (tejedor)
Parameters: - t (np.array) – time
- x (np.array) – x-position
- y (np.array) – y-position
Returns: [:,0]
: lag time[:,1]
: MSD[:,2]
: Mean displacement moment of 4th order[:,3]
: MME[:,4]
: Mean maximal excursion of 4th order
Return type: np.array of size
(l_max,5)
spt.special¶
Some special functions, e.g. track splitting into subtrajectories, generation of track and diffusion maps, …
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spt.special.
apply_multiply_jumps
(df, factor, segment, ratio)¶ Groupby apply approach of multiply_jumptimes(df,factor,segment,ratio) to each group in
df
.Parameters: - df (pandas.DataFrame) – (Complete) linked localizations as returned by spt.mob_props.main() (pickedXXXX.hdf5 files)
- factor (int) – Jumptime multiplication factor
- segment (int) – Number of localizations within segments.
- ratio (int) – Ratio of slowed down to normal segments (see above).
Returns: Same as
df
but with modified jumptimes.Return type: df_mod (TYPE)
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spt.special.
assign_prop_to_picked
(props, picked, field='a_iter')¶
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spt.special.
assign_subgroup
(df, subN)¶ Splitting of
supgroup
(full trajectory ID) intosubgroup
(subtrajectory ID). Each subgroup splits the supgroup in chunks ofsubN
, i.e. the subtrajectory duration. Subtrajectories with less then 10 localizations are dropped.Parameters: - df (pandas.DataFrame) – One trajectory as returned by spt.mob_props.main() (i.e. one group in pickedXXXX.hdf5 files)
- subN (int) – Maximum length of sub-trajectories
Returns: Same as
df
but with one new columnsubgroup
(subtrajectory ID) in chunks ofsubN
. See also above.Return type: pandas.DataFrame
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spt.special.
get_trackmap
(locs, fov, oversampling, field='assign_field')¶
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spt.special.
multiply_jumps
(df, factor, segment, ratio)¶ Multiply jumps by
sqrt(factor)
such that segments will have a diffusion contant multiplied byfactor
. Segments number of localizations is given bysegment
. Ratio indicates how many segments are mutiplied, i.e. forratio=2
every 2nd, forratio=3
every third segment is multiplied.Parameters: - df (pandas.DataFrame) – One trajectory as returned by spt.mob_props.main() (i.e. one group in pickedXXXX.hdf5 files)
- factor (int) – Diffusion constant multiplication factor, i.e. jumps will mutliplied by sqrt(factor) !!
- segment (int) – Number of localizations within segments.
- ratio (int) – Ratio of multiplied to normal segments (see above).
Returns: Same as
df
but with modified jumptimes.Return type: pandas.DataFrame
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spt.special.
multiply_jumptimes
(df, factor, segment, ratio)¶ Multiply jumptimes by
factor
in segments. Segments number of localizations is given bysegment
. Ratio indicates how many segments are mutiplied, i.e. forratio=2
every 2nd, forratio=3
every third segment is multiplied leading to apparent slower diffusion within these segments.Parameters: - df (pandas.DataFrame) – One trajectory as returned by spt.mob_props.main() (i.e. one group in pickedXXXX.hdf5 files)
- factor (int) – Jumptime multiplication factor
- segment (int) – Number of localizations within segments.
- ratio (int) – Ratio of slowed down to normal segments (see above).
Returns: Same as
df
but with modified jumptimes.Return type: pandas.DataFrame
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spt.special.
render_trackmap
¶
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spt.special.
split_trajectories
(df, subN)¶ Groupby apply approach of assign_subgroup(df,subN) to each group in
df
. Splits trajectories into shorter trajectories of lengthsubN
. Three new columns are assigned to give track ID:supgroup
: Super-group = group column of originalsubgroup
: Sub-group = New trajectories of length subN or lowergroup
: Unique new sub-group IDParameters: - df (pandas.DataFrame) – (Complete) linked localizations as returned by spt.mob_props.main() (pickedXXXX.hdf5 files)
- subN (int) – Maximum length of sub-trajectories
Returns: Same as
df
but with new columns indicating sup(er)- or subtrajectories. See above.Return type: pandas.DataFrame