asap.dataimport package

Submodules

asap.dataimport.apply_mipmaps_to_render module

class asap.dataimport.apply_mipmaps_to_render.AddMipMapsToStack(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 AddMipMapsToStackParameters

default_output_schema

alias of AddMipMapsToStackOutput

default_schema

alias of AddMipMapsToStackParameters

run()

asap.dataimport.apply_mipmaps_to_render.addMipMapsToRender(render, input_stack, mipmap_prefix, imgformat, levels, z)

asap.dataimport.create_mipmaps module

exception asap.dataimport.create_mipmaps.CreateMipMapException

Bases: RenderModuleException

Exception raised when there is a problem creating a mipmap

asap.dataimport.create_mipmaps.create_mipmaps(inputImage, outputDirectory='.', *args, **kwargs)

legacy create_mipmaps function

asap.dataimport.create_mipmaps.create_mipmaps_legacy(inputImage, outputDirectory='.', *args, **kwargs)

legacy create_mipmaps function

asap.dataimport.create_mipmaps.create_mipmaps_uri(inputImage, outputDirectory=None, method='block_reduce', mipmaplevels=[1, 2, 3], outputformat='tif', convertTo8bit=True, force_redo=True, **kwargs)

function to create downsampled images from an input image

Parameters

• inputImage (str) – path to input image

• outputDirectory (str) – path to save output images (default to current directory)

• mipmaplevels (list or tuple) – list or tuple of integers (default to (1,2,3))

• outputformat (str) – string representation of extension of image format (default tif)

• convertTo8bit (boolean) – whether to convert the image to 8 bit, dividing each value by 255

• force_redo (boolean) – whether to recreate mip map images if they already exist

• method (str) – string corresponding to downsampling method

• block_func (str) – string corresponding to function used by block_reduce

• ds_filter (str) – string corresponding to PIL downsample mode

Returns

list of output images created in order of levels

Return type

list

Raises

MipMapException – if an image cannot be created for some reason

asap.dataimport.create_mipmaps.mipmap_PIL(im, levels_file_map, ds_filter='NEAREST', force_redo=True, **kwargs)

asap.dataimport.create_mipmaps.mipmap_block_reduce(im, levels_file_map, block_func='mean', force_redo=True, **kwargs)

asap.dataimport.create_mipmaps.writeImage(img, outpath, force_redo)

asap.dataimport.generate_EM_tilespecs_from_metafile module

create tilespecs from TEMCA metadata file

class asap.dataimport.generate_EM_tilespecs_from_metafile.GenerateEMTileSpecsModule(schema_type=None, *args, **kwargs)

Bases: StackOutputModule

Note

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

default_output_schema

alias of GenerateEMTileSpecsOutput

default_schema

alias of GenerateEMTileSpecsParameters

static image_coords_from_stage(stage_coords, resX, resY, rotation)

run()

static sectionId_from_z(z)

tileId_from_basename(fname)

ts_from_imgdata(imgdata, imgprefix, x, y, minint=0, maxint=255, maskUrl=None, width=3840, height=3840, z=None, sectionId=None, scopeId=None, cameraId=None, pixelsize=None)

asap.dataimport.generate_mipmaps module

class asap.dataimport.generate_mipmaps.GenerateMipMaps(schema_type=None, *args, **kwargs)

Bases: StackInputModule

Note

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

default_output_schema

alias of GenerateMipMapsOutput

default_schema

alias of GenerateMipMapsParameters

run()

asap.dataimport.generate_mipmaps.create_mipmap_from_tuple(mipmap_tuple, levels=[1, 2, 3], imgformat='tif', convertTo8bit=True, force_redo=True, **kwargs)

asap.dataimport.generate_mipmaps.create_mipmap_from_tuple_uri(mipmap_tuple, levels=[1, 2, 3], imgformat='tif', convertTo8bit=True, force_redo=True, **kwargs)

asap.dataimport.generate_mipmaps.get_filepath_from_tilespec(ts)

asap.dataimport.generate_mipmaps.make_tilespecs_and_cmds(render, inputStack, output_prefix, zvalues, levels, imgformat, convert_to_8bit, force_redo, pool_size, method)

asap.dataimport.make_montage_scapes_stack module

class asap.dataimport.make_montage_scapes_stack.MakeMontageScapeSectionStack(schema_type=None, *args, **kwargs)

Bases: StackOutputModule

Note

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

default_output_schema

alias of MakeMontageScapeSectionStackOutput

default_schema

alias of MakeMontageScapeSectionStackParameters

run()

asap.dataimport.make_montage_scapes_stack.create_montage_scape_tile_specs(render, input_stack, image_directory, scale, project, tagstr, imgformat, Z, apply_scale=False, uuid_prefix=True, uuid_prefix_length=10, **kwargs)

asap.dataimport.schemas module

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

Bases: DefaultSchema

AddMipMapsToStackOutput

key	description	default	field_type	json_type
output_stack	no description	(REQUIRED)	String	str
missing_ts_zs	Z values for which apply mipmaps failed	[]	List	int

opts = <marshmallow.schema.SchemaOpts object>

class asap.dataimport.schemas.AddMipMapsToStackParameters(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

AddMipMapsToStackParameters

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
mipmap_dir	directory to which the mipmaps will be stored	NA	InputDir	str
mipmap_prefix	uri prefix from which mipmap locations are built.	(REQUIRED)	String	str
levels	number of levels of mipmaps, default is 6	6	Integer	int
imgformat	mipmap image format, default is tiff	tiff	String	str

mipmap_directory_to_prefix(data)

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

GenerateEMTileSpecsOutput

key	description	default	field_type	json_type
stack	stack to which generated tiles were added	(REQUIRED)	String	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: OutputStackParameters

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

GenerateEMTileSpecsParameters

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
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
metafile	metadata file containing TEMCA acquisition data	NA	InputFile	str
metafile_uri	uri of metadata containing TEMCA acquisition data	(REQUIRED)	String	str
maskUrl	absolute path to image mask to apply	None	InputFile	str
maskUrl_uri	uri of image mask to apply	None	String	str
image_directory	directory used in determining absolute paths to images. Defaults to parent directory containing metafile if omitted.	NA	InputDir	str
image_prefix	prefix used in determining full uris of images in metadata. Defaults to using the / delimited prefix to the metadata_uri if omitted	NA	String	str
maximum_intensity	intensity value to interpret as white	255	Integer	int
minimum_intensity	intensity value to interpret as black	0	Integer	int
sectionId	sectionId to apply to tiles during ingest. If unspecified will default to a string representation of the float value of z_index.	NA	String	str

image_directory_to_prefix(data)

maskUrl_to_uri(data)

metafile_to_uri(data)

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

GenerateMipMapsOutput

key	description	default	field_type	json_type
levels	no description	(REQUIRED)	Integer	int
output_prefix	no description	(REQUIRED)	String	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: InputStackParameters

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

GenerateMipMapsParameters

key	description	default	field_type	json_type
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_dir	directory to which the mipmaps will be stored	NA	String	str
output_prefix	uri prefix for generated mipmaps	(REQUIRED)	String	str
method	method to downsample mipmapLevels, ‘PIL’ for PIL Image (currently NEAREST) filtered resize, can be ‘block_reduce’ for skimage based area downsampling	block_reduce	String	str
convert_to_8bit	convert the data from 16 to 8 bit (default True)	True	Boolean	bool
pool_size	number of cores to be used	20	Integer	int
imgformat	image format for mipmaps (default tiff)	tiff	String	str
levels	number of levels of mipmaps, default is 6	6	Integer	int
force_redo	force re-generation of existing mipmaps	True	Boolean	bool
PIL_filter	filter to be used in PIL resize	NEAREST	String	str
block_func	function to represent blocks in area downsampling with block_reduce	mean	String	str

directory_to_prefix(data)

opts = <marshmallow.schema.SchemaOpts object>

classmethod validationOptions(options)

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

Bases: DefaultSchema

MakeMontageScapeSectionStackOutput

key	description	default	field_type	json_type
output_stack	Name of the downsampled sections stack	(REQUIRED)	String	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: OutputStackParameters

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

MakeMontageScapeSectionStackParameters

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
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
montage_stack	stack to make a downsample version of	(REQUIRED)	String	str
image_directory	directory that stores the montage scapes	(REQUIRED)	String	str
set_new_z	set to assign new z values starting from 0 (default - False)	False	Boolean	bool
new_z_start	new starting z index	0	Integer	int
remap_section_ids	change section ids to new z values. default = False	False	Boolean	bool
imgformat	image format of the montage scapes (default - tif)	tif	String	str
scale	scale of montage scapes	(REQUIRED)	Float	float
apply_scale	Do you want to scale the downsample to the size of section? Default = False	False	Boolean	bool
doFilter	whether to apply default filtering when generating missing downsamples	True	Boolean	bool
level	integer mipMapLevel used to generate missing downsamples	1	Integer	int
fillWithNoise	Whether to fill the background pixels with noise when generating missing downsamples	False	Boolean	bool
memGB_materialize	Java heap size in GB for materialization	12G	String	str
pool_size_materialize	number of processes to generate missing downsamples	1	Integer	int
filterListName	Apply specified filter list to all renderings	NA	String	str
uuid_prefix	Prepend uuid to generated tileIds to prevent collisions	True	Boolean	bool
uuid_length	length of uuid4 string used in uuid prefix	10	Integer	int

opts = <marshmallow.schema.SchemaOpts object>

validate_data(data)

Module contents