asap.intensity_correction package

Submodules

asap.intensity_correction.apply_multiplicative_correction module

class asap.intensity_correction.apply_multiplicative_correction.MultIntensityCorr(schema_type=None, *args, **kwargs)

Bases: StackTransitionModule

Note

This class takes a ArgSchema as an input to parse inputs , with a default schema of type MultIntensityCorrParams

default_schema

alias of MultIntensityCorrParams

run()

asap.intensity_correction.apply_multiplicative_correction.getImage(ts, channel=None)

Simple function to get the level 0 image of this tilespec as a numpy array

Parameters

• ts (renderapi.tilespec.TileSpec) – tilespec to get images from (presently assumes this is a tiff image whose URL can be read with tifffile)

• channel (str) – channel name to get image of, default=None which will default to the non channel image pyramid

Returns

2d numpy array of this image

Return type

numpy.array

asap.intensity_correction.apply_multiplicative_correction.intensity_corr(img, ff, clip, scale_factor, clip_min, clip_max)

utility function to correct an image with a flatfield correction will take img and return img_out = img * max(ff) / (ff + .0001) converted back to the original type of img

Parameters

• img (numpy.array) – N,M array to correct, could be any type

• ff (numpy.array) – N,M array of flatfield correction, could be of any type

Returns

N,M numpy array of the same type as img but now corrected

Return type

numpy.array

asap.intensity_correction.apply_multiplicative_correction.process_tile(C, dirout, stackname, clip, scale_factor, clip_min, clip_max, input_ts, corr_dict=None)

function to correct each tile in the input_ts with the matrix C, and potentially move the original tiles to a new location.abs

Parameters

• C (numpy.array) – a 2d numpy array of uint16 or uint8 that represents the correction to apply

• corr_dict (dict or None) – a dictionary with keys of strings of channel names and values of corrections (as with C). If None, C will be applied to each channel, if they exist.

• dirout (str) – the path to the directory to save all corrected images

• input_ts (renderapi.tilespec.TileSpec) – the tilespec with the tiles to be corrected

asap.intensity_correction.apply_multiplicative_correction.write_image(dirout, orig_imageurl, Res, stackname, z)

asap.intensity_correction.calculate_multiplicative_correction module

class asap.intensity_correction.calculate_multiplicative_correction.MakeMedian(schema_type=None, *args, **kwargs)

Bases: RenderModule

Note

This class takes a ArgSchema as an input to parse inputs , with a default schema of type MakeMedianParams

default_schema

alias of MakeMedianParams

run()

asap.intensity_correction.calculate_multiplicative_correction.getImageFromTilespecs(alltilespecs, index, channel=None)

asap.intensity_correction.calculate_multiplicative_correction.make_median_image(alltilespecs, numtiles, outImage, pool_size, chan=None, gauss_size=10)

asap.intensity_correction.calculate_multiplicative_correction.randomly_subsample_tilespecs(alltilespecs, numtiles)

asap.intensity_correction.schemas module

class asap.intensity_correction.schemas.MakeMedianParams(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: StackTransitionParameters

This schema is designed to be a schema_type for an ArgSchemaParser object

MakeMedianParams

key	description	default	field_type	json_type
pool_size	no description	1	Integer	int
minZ	no description	NA	Integer	int
maxZ	no description	NA	Integer	int
z	no description	NA	Integer	int
zValues	no description	NA	List	int
input_json	file path of input json file	NA	InputFile	str
output_json	file path to output json file	NA	OutputFile	str
log_level	set the logging level of the module	ERROR	LogLevel	str
render	parameters to connect to render server	(REQUIRED)	RenderClientParameters	dict
input_stack	no description	(REQUIRED)	String	str
output_stack	no description	(REQUIRED)	String	str
close_stack	no description	False	Boolean	bool
overwrite_zlayer	no description	False	Boolean	bool
output_stackVersion	no description	NA	RenderStackVersion	dict
file_prefix	File prefix for median image file that is saved	Median	String	str
output_directory	Output Directory for saving median image	(REQUIRED)	String	str
num_images	Number of images to randomly subsample to generate median	-1	Integer	int

opts = <marshmallow.schema.SchemaOpts object>

class asap.intensity_correction.schemas.MultIntensityCorrParams(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: StackTransitionParameters

This schema is designed to be a schema_type for an ArgSchemaParser object

MultIntensityCorrParams

key	description	default	field_type	json_type
pool_size	no description	1	Integer	int
minZ	no description	NA	Integer	int
maxZ	no description	NA	Integer	int
z	no description	NA	Integer	int
zValues	no description	NA	List	int
input_json	file path of input json file	NA	InputFile	str
output_json	file path to output json file	NA	OutputFile	str
log_level	set the logging level of the module	ERROR	LogLevel	str
render	parameters to connect to render server	(REQUIRED)	RenderClientParameters	dict
input_stack	no description	(REQUIRED)	String	str
output_stack	no description	(REQUIRED)	String	str
close_stack	no description	False	Boolean	bool
overwrite_zlayer	no description	False	Boolean	bool
output_stackVersion	no description	NA	RenderStackVersion	dict
correction_stack	Correction stack (usually median stack for AT data)	(REQUIRED)	String	str
output_directory	Directory for storing Images	(REQUIRED)	OutputDir	str
cycle_number	what cycleNumber to upload for output_stack on render	2	Integer	int
cycle_step_number	what cycleStepNumber to upload for output_stack on render	1	Integer	int
clip	whether to clip values	True	Boolean	bool
scale_factor	scaling value	1.0	Float	float
clip_min	Min Clip value	0	Integer	int
clip_max	Max Clip value	65535	Integer	int

opts = <marshmallow.schema.SchemaOpts object>

Module contents