Annotation Methods¶
- particletracker.annotate.annotation_methods.boxes(frame, data, f, parameters=None, call_num=None)¶
Boxes places a rotated rectangle on the image that encloses the contours of specified particles.
Notes
This method requires you to have used contours for the tracking and run boxes in postprocessing.
- Parameters
cmap_type – Options are ‘static’ or ‘dynamic’
cmap_column – Name of column containing data to specify colour in dynamic mode,
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_scale – Scale factor for colour map
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
classifier_column – None selects all particles, column name of classifier values to specify subset of particles
classifier – The value in the classifier column which applies to subset (True or False)
thickness – Thickness of box. -1 fills the box in
frame – This is the unmodified frame of the input movie
data – This is the dataframe that stores all the tracked data
f – frame index
parameters – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.circles(frame, data, f, parameters=None, call_num=None)¶
Circles places a ring on every specified particle
- Parameters
xdata_column – Name of column to use for x coordinates
ydata_column – Name of column to use for y coordinates
rad_from_data – Specify radius manually: False or use measured rad: True. Only works for Hough transform.
radius – If rad_from_data = False this specifies the radius of circle
cmap_type – Options are static or dynamic
cmap_column – Name of column containing data to specify colour in dynamic mode,#for dynamic
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_scale – Scale factor for colour map
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
classifier_column – None - selects all particles, column name of classifier values to apply to subset of particles
classifier – The value in the classifier column to apply colour map to (True or False)
thickness – Thickness of circle. -1 fills the circle in solidly.
frame (np.ndarray) – This is the unmodified frame of the input movie
data (pandas dataframe) – This is the dataframe that stores all the tracked data
f (int) – frame index
parameters (dict) – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num (int or None) – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.contours(frame, data, f, parameters=None, call_num=None)¶
Contours draws the tracked contour returned from Contours tracking method onto the image.
Notes
Requires the contours tracking method.
- Parameters
cmap_type – Options are static or dynamic
cmap_column – Name of column containing data to specify colour in dynamic mode
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_scale – Scale factor for colour map
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
classifier_column – None - selects all particles, column name of classifier values to apply to subset of particles
classifier – The value in the classifier column to apply colour map to (True or False).
thickness – Thickness of contour. -1 will fill in contour
frame – This is the unmodified frame of the input movie
data – This is the dataframe that stores all the tracked data
f – frame index
parameters – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.networks(frame, data, f, parameters=None, call_num=None)¶
Networks draws a network of lines between particles
Notes
The network must previously have been calculated in postprocessing. See “neighbours” in postprocessing.
- Parameters
cmap_type – Options are static or dynamic
cmap_column – Name of column containing data to specify colour in dynamic mode,#for dynamic
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_scale – Scale factor for colour map
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
classifier_column – None - selects all particles, column name of classifier values to apply to subset of particles
classifier – The value in the classifier column to apply colour map to.
thickness – Thickness of network lines
frame (np.ndarray) – This is the unmodified frame of the input movie
data (pandas dataframe) – This is the dataframe that stores all the tracked data
f (int) – frame index
parameters (dict) – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num (int or None) – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.particle_labels(frame, data, f, parameters=None, call_num=None)¶
Annotates image with particle info from one column. The most common use is to indicate the particle index but any column of data could be used.
Notes
For particle ids to be meaningful, you must have already run ‘processed part’ with linking selected. This is particularly useful if you want to extract information about specific particles. Annotate their ids to identify the reference id of the one you are interested in and then you can pull the subset of processed data out. See examples in Jupyter notebook. Any particle level data can however be displayed.
- Parameters
values_column – Name of column containing particle info to be displayed.
position – Coordinates of upper left corner of text
font_colour – Colour of font specified in (B,G,R) format where values are integers from 0-255
font_size – Size of font
font_thickness – Thickness of font
frame – This is the unmodified frame of the input movie
data – This is the dataframe that stores all the tracked data
f – frame index
parameters – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.text_label(frame, data, f, parameters=None, call_num=None)¶
Text labels place a static label on an image at specific location.
Notes
This function is for adding titles or info that doesn’t change
- Parameters
text – Text to be displayed
position – Coordinates of upper left corner of text
font_colour – Colour of font specified in (B,G,R) format where values are integers from 0-255
font_size – Size of font
font_thickness – Thickness of font
frame – This is the unmodified frame of the input movie
data – This is the dataframe that stores all the tracked data
f – frame index
parameters – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.trajectories(frame, data, f, parameters=None, call_num=None)¶
Trajectories draws the historical track of each particle onto an image.
Notes
Requires data from other frames hence you must have previously processed the video and then toggled use_part_processed button.
- Parameters
x_column – column name of x coordinates of particle,
y_column – column name of y coordinates of particle,
traj_length – number of historical frames to include in each trajectory.
classifier_column – None - selects all particles, column name of classifier values to apply to subset of particles
classifier – The value in the classifier column to apply colour map to (True or False).
cmap_type – Options are static or dynamic
cmap_column – Name of column containing data to specify colour in dynamic mode,
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_min – Specifies min data value for colour map in dynamic mode
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
thickness – Thickness of line.
frame (np.ndarray) – This is the unmodified frame of the input movie
data (pandas dataframe) – This is the dataframe that stores all the tracked data
f (int) – frame index
parameters (dict) – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num (int or None) – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.var_label(frame, data, f, parameters=None, call_num=None)¶
Var labels puts text on an image at specific location for each frame. The value displayed in that frame is mapped to a column in the dataframe. The values next to each frame should all be the same for that column. Use for example to specify the temperature.
Notes
This function is for adding data specific to a single frame. For example you could indicate the temperature of the sample or time. The data for a given frame should be stored in a particular column specified in the ‘var_column’ section of the dictionary.
- Parameters
var_column – Column name containing the info to be displayed on each frame
position – Coordinates of upper left corner of text
font_colour – Colour of font specified in (B,G,R) format where values are integers from 0-255
font_size – Size of font
font_thickness – Thickness of font
frame – This is the unmodified frame of the input movie
data – This is the dataframe that stores all the tracked data
f – frame index
parameters – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.vectors(frame, data, f, parameters=None, call_num=None)¶
Vectors draw info onto images in the form of arrows.
Notes
Vectors draws an arrow starting at each particle with a length and direction specified by 2 components. The magnitude of the vector can be scaled to be appropriate.
- Parameters
dx_column – Column name of x component of vector, defaults to ‘x’
dy_column – Column name of y component of vector, defaults to ‘y’
vector_scale – scaling between vector data and length of displayed line
classifier_column – None - selects all particles, column name of classifier values to apply to subset of particles
classifier – The value in the classifier column to apply colour map to.
cmap_type – Options are static or dynamic
cmap_column – Name of column containing data to specify colour in dynamic mode,
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_min – Specifies min data value for colour map in dynamic mode
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
line_type – OpenCV parameter can be -1, 4, 8, 16
thickness – Thickness of line. Defaults to 2
tip_length – Controls length of arrow head
frame (np.ndarray) – This is the unmodified frame of the input movie
data (pandas dataframe) – This is the dataframe that stores all the tracked data
f (int) – frame index
parameters (dict) – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num (int or None) – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray
- particletracker.annotate.annotation_methods.voronoi(frame, data, f, parameters=None, call_num=None)¶
Voronoi draws the voronoi network that surrounds each particle
Notes
The voronoi cells must previously have been calculated in postprocessing. See “voronoi” in postprocessing.
- Parameters
cmap_type – Options are static or dynamic
cmap_column – Name of column containing data to specify colour in dynamic mode,#for dynamic
cmap_max – Specifies max data value for colour map in dynamic mode
cmap_min – Specifies min data value for colour map in dynamic mode
cmap_scale – Scale factor for colour map
colour – Colour to be used for static cmap_type (B,G,R) values from 0-255
classifier_column – None - selects all particles, column name of classifier values to apply to subset of particles
classifier – The value in the classifier column to apply colour map to.
thickness – Thickness of network lines
frame (np.ndarray) – This is the unmodified frame of the input movie
data (pandas dataframe) – This is the dataframe that stores all the tracked data
f (int) – frame index
parameters (dict) – Nested dictionary like object (same as .param files or output from general.param_file_creator.py)
call_num (int or None) – Usually None but if multiple calls are made modifies method name with get_method_key
- Returns
annotated frame
- Return type
np.ndarray