leicascanningtemplate API reference

class leicascanningtemplate.ScanningTemplate(filename)

Bases: object

Python object of Leica LAS Matrix Screener Scanning Template XML. Provides easy access to elements via attributes:

>>> tmpl = ScanningTemplate('{ScanningTemplate}tmpl.xml')
>>> # attributes of MatrixScreenerTemplate/ScanningTemplate/Properties
>>> print(tmpl.properties.attrib)

Parameters:filename (str) – XML to load.

filename

str

Path XML-filename.

root

lxml.objectify.ObjectifiedElement

Objectified root of loaded XML. See http://lxml.de/objectify.html#the-lxml-objectify-api

add_well(well_x, well_y, start_x, start_y)

Add well with associated scan fields. self.wells[0] and self.fields[0] will be used as base. ScanWellData will be added to ScanWellArray and ScanFieldData to ScanFieldArray. The amount of fields added is decided by Properties/CountOfScanFields.

Parameters:

• well_x (int) –
• well_y (int) –
• start_x (int) – In meters. FieldXCoordinate of first field in well.
• start_y (int) – In meters. FieldYCoordinate of first field in well.

Raises:

ValueError – If well or fields already exists.

count_of_assigned_jobs

Number of fields that have attrib[‘JobAssigned’] set to true.

count_of_wells

Number of wells in x/y-direction of template.

Returns:(xs, ys) number of wells in x and y direction. Return type:tuple

field(well_x=1, well_y=1, field_x=1, field_y=1)

ScanFieldData of specified field.

Parameters:

• well_x (int) –
• well_y (int) –
• field_x (int) –
• field_y (int) –

Returns:

ScanFieldArray/ScanFieldData element.

Return type:

lxml.objectify.ObjectifiedElement

field_array

Short hand for self.root.ScanFieldArray

field_exists(well_x, well_y, field_x, field_y)

Check if field exists ScanFieldArray.

fields

All ScanFieldData elements.

Returns: Return type:list of objectify.ObjectifiedElement

move_well(well_x, well_y, start_x, start_y)

Move well and associated scan fields. Spacing between fields will be what Properties/ScanFieldStageDistance is set to.

Parameters:

• well_x (int) –
• well_y (int) –
• start_x (int) – In meters. FieldXCoordinate of first field in well.
• start_y (int) – In meters. FieldYCoordinate of first field in well.

Raises:

ValueError – If specified well or associated fields does not exist.

properties

Short hand for self.root.ScanningTemplate.Properties

remove_well(well_x, well_y)

Remove well and associated scan fields.

Parameters:

• well_x (int) –
• well_y (int) –

Raises:

AttributeError – If well not found.

update_counts()

Update counts of fields and wells.

update_start_position()

Set start position of experiment to position of first field.

update_well_positions()

Set well_attrib['FieldXStartCoordinate'] and well_attrib['FieldYStartCoordinate'] to FieldXCoordinate and FieldYCoordinate of first field in well.

well(well_x=1, well_y=1)

ScanWellData of specific well.

Parameters:

• well_x (int) –
• well_y (int) –

Returns:

Return type:

lxml.objectify.ObjectifiedElement

well_array

Short hand for self.root.ScanWellArray

well_attrib(well_x=1, well_y=1)

Attributes of specific well.

Parameters:

• well_x (int) –
• well_y (int) –

Returns:

Attributes of ScanWellArray/ScanWellData.

Return type:

dict

well_exists(well_x, well_y)

Check if well exists in ScanWellArray.

well_fields(well_x=1, well_y=1)

All ScanFieldData elements of given well.

Parameters:

• well_x (int) –
• well_y (int) –

Returns:

All ScanFieldData elements of given well.

Return type:

list of lxml.objectify.ObjectifiedElement

wells

All ScanWellData elements.

Returns: Return type:list of objectify.ObjectifiedElement

write(filename=None)

Save template to xml. Before saving template will update date, start position, well positions, and counts.

Parameters:filename (str) – If not set, XML will be written to self.filename.