lumicks.pylake.kymo.Kymo¶
- class Kymo(name, file, start, stop, metadata, position_offset=0, calibration=None)¶
A Kymograph exported from Bluelake
- Parameters
name (str) – Kymograph name
file (lumicks.pylake.File) – Parent file. Contains the channel data.
start (int) – Start point in the relevant info wave.
stop (int) – End point in the relevant info wave.
metadata (ScanMetaData) – Metadata for this Kymo.
position_offset (float) – Coordinate position offset with respect to the original raw data.
calibration (PositionCalibration) – Class defining calibration from microns to desired position units.
- __getitem__(item)¶
All indexing is in timestamp units (ns)
- calibrate_to_kbp(length_kbp)¶
Calibrate from microns to other units.
- Parameters
length (float) – length of the kymo in kilobase pairs
- crop_and_calibrate(channel='rgb', tether_length_kbp=None, **kwargs)¶
Open a widget to interactively edit the image stack.
Actions
left-click and drag to define the cropped ROI
- Parameters
channel ('rgb', 'red', 'green', 'blue', None; optional) – Channel to plot for RGB images (None defaults to ‘rgb’) Not used for grayscale images
tether_length_kbp (float) – Length of the tether in the cropped region in kilobase pairs. If provided, the kymo returned from the
image
property will be automatically calibrated to this tether length.**kwargs – Forwarded to
Kymo.plot()
.
Examples
from lumicks import pylake import matplotlib.pyplot as plt # Loading a stack. h5_file = pylake.File("example.h5") _, kymo = h5_file.kymos.popitem() widget = kymo.crop_and_calibrate("green", 48.502) plt.show() # Select cropping ROI by left-click drag # Grab the updated image stack new_kymo = widget.kymo
- crop_by_distance(lower, upper)¶
Crop the kymo by position.
Crops the kymograph down to lower <= x < upper.
- downsampled_by(time_factor=1, position_factor=1, reduce=<function sum>)¶
Return a copy of this Kymograph which is downsampled by
time_factor
in time andposition_factor
in space.
- export_tiff(filename, *, dtype=<class 'numpy.float32'>, clip=False)¶
Save the RGB photon counts to a TIFF image
- Parameters
filename (str) – The name of the TIFF file where the image will be saved.
dtype (np.dtype) – The data type of a single color channel in the resulting image.
clip (bool) – If enabled, the photon count data will be clipped to fit into the desired
dtype
. This option is disabled by default: an error will be raise if the data does not fit.
- classmethod from_dataset(h5py_dset, file)¶
Construct a confocal class from dataset.
- Parameters
h5py_dset (h5py.Dataset) – The original HDF5 dataset containing confocal scan information
file (lumicks.pylake.File) – The parent file. Used to loop up channel data
- get_image(channel='rgb') numpy.ndarray ¶
Get image data for the full stack as an
np.ndarray
.- Parameters
channel ({'red', 'green', 'blue', 'rgb'}) – The color channel of the requested data.
- line_timestamp_ranges(exclude=None, *, include_dead_time=None)¶
Get start and stop timestamp of each line in the kymo.
Note: The stop timestamp for each line is defined as the first sample past the end of the relevant data such that the timestamps can be used for slicing directly.
- plot(channel, axes=None, **kwargs)¶
Show a formatted plot for the requested color channel.
- Parameters
channel ({'red', 'green', 'blue', 'rgb'}) – Color channel to plot.
axes (mpl.axes.Axes or None) – If supplied, the axes instance in which to plot.
**kwargs – Forwarded to
matplotlib.pyplot.plot()
ormatplotlib.pyplot.imshow()
- plot_blue(**kwargs)¶
Plot an image of the blue photon channel
Deprecated since version 0.11.1:
plot_blue()
is deprecated. Useplot(channel='blue')
instead.
- plot_green(**kwargs)¶
Plot an image of the green photon channel
Deprecated since version 0.11.1:
plot_green()
is deprecated. Useplot(channel='green')
instead.
- plot_red(**kwargs)¶
Plot an image of the red photon channel
Deprecated since version 0.11.1:
plot_red()
is deprecated. Useplot(channel='red')
instead.
- plot_rgb(**kwargs)¶
Plot an image of all color channels.
Deprecated since version 0.11.1:
plot_rgb()
is deprecated. Useplot(channel='rgb')
instead.
- plot_with_force(force_channel, color_channel, aspect_ratio=0.25, reduce=<function mean>, kymo_args={}, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, **kwargs)¶
Plot kymo with force channel downsampled over scan lines
Note that high frequency channel data must be available for this function to work.
- Parameters
force_channel (str) – name of force channel to downsample and plot (e.g. ‘1x’)
color_channel (str) – color channel of kymo to plot (‘red’, ‘green’, ‘blue’, ‘rgb’)
aspect_ratio (float) – aspect ratio of the axes (i.e. ratio of y-unit to x-unit)
reduce (callable) – The
numpy
function which is going to reduce multiple samples into one. Forwarded toSlice.downsampled_over()
kymo_args (dict) – Forwarded to
matplotlib.pyplot.imshow()
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
**kwargs – Forwarded to
Slice.plot()
.
- plot_with_position_histogram(color_channel, pixels_per_bin=1, hist_ratio=0.25, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, **kwargs)¶
Plot kymo with histogram along position axis
- Parameters
color_channel (str) – color channel of kymo to plot (‘red’, ‘green’, ‘blue’, ‘rgb’).
pixels_per_bin (int) – number of pixels along position axis to bin together.
hist_ratio (float) – width of the histogram with respect to the kymo image.
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
**kwargs – Forwarded to histogram bar plot.
- plot_with_time_histogram(color_channel, pixels_per_bin=1, hist_ratio=0.25, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, **kwargs)¶
Plot kymo with histogram along time axis
- Parameters
color_channel (str) – color channel of kymo to plot (‘red’, ‘green’, ‘blue’, ‘rgb’).
pixels_per_bin (int) – number of pixels along time axis to bin together.
hist_ratio (float) – height of the histogram with respect to the kymo image.
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
**kwargs – Forwarded to histogram bar plot.
- save_tiff(filename, dtype=<class 'numpy.float32'>, clip=False)¶
Deprecated since version 0.13.0: This method has been renamed to
export_tiff
to more accurately reflect that it is exporting to a different format.
- property blue_image¶
Returns an image representing the blue channel
Deprecated since version 0.12.0: This property will be removed in a future release. Use
get_image('blue')
instead.
- property center_point_um¶
Returns a dictionary of the x/y/z center coordinates of the scan (w.r.t. brightfield field of view)
- property green_image¶
Returns an image representing the green channel
Deprecated since version 0.12.0: This property will be removed in a future release. Use
get_image('green')
instead.
- property line_time_seconds¶
Line time in seconds
- property pixel_time_seconds¶
Pixel dwell time in seconds
- property pixelsize¶
Returns a
List
of axes dimensions in calibrated units. The length of the list corresponds to the number of scan axes.
- property pixelsize_um¶
Returns a
List
of axes dimensions in um. The length of the list corresponds to the number of scan axes.
- property red_image¶
Returns an image representing the red channel
Deprecated since version 0.12.0: This property will be removed in a future release. Use
get_image('red')
instead.
- property rgb_image¶
Returns an rgb image
Deprecated since version 0.12.0: This property will be removed in a future release. Use
get_image('rgb')
instead.
- property shape¶
Shape of the reconstructed
Kymo
image
- property size_um¶
Returns a
List
of scan sizes in um along axes. The length of the list corresponds to the number of scan axes.
- property timestamps: numpy.ndarray¶
Timestamps for each image pixel.
The returned array has the same shape as the
color_image
arrays. Timestamps are defined at the mean of the timestamps.