asap.rough_align package

Submodules

asap.rough_align.apply_rough_alignment_to_montages module

exception asap.rough_align.apply_rough_alignment_to_montages.ApplyRoughAlignmentException

Bases: RenderModuleException

Something is wrong in ApplyRough….

class asap.rough_align.apply_rough_alignment_to_montages.ApplyRoughAlignmentTransform(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 ApplyRoughAlignmentTransformParameters

default_output_schema

alias of ApplyRoughAlignmentOutputParameters

default_schema

alias of ApplyRoughAlignmentTransformParameters

run()

asap.rough_align.apply_rough_alignment_to_montages.add_masks_to_lowres(render, stack, z, mask_map)

asap.rough_align.apply_rough_alignment_to_montages.apply_rough_alignment(render, input_stack, prealigned_stack, lowres_stack, output_stack, output_dir, scale, mask_input_dir, update_lowres_with_masks, read_masks_from_lowres_stack, filter_montage_output_with_masks, mask_exts, Z, apply_scale=False, consolidateTransforms=True, remap_section_ids=False)

asap.rough_align.apply_rough_alignment_to_montages.filter_highres_with_masks(resolved_highres, tspec_lowres, mask_map)

function to return a filtered list of tilespecs from a

ResolvedTiles object, based on a lowres mask

Parameters

• resolved_highres (renderapi.resolvedtiles.ResolvedTiles object) – tilespecs and transforms from a single section

• tspec_lowres (renderapi.tilespec.TileSpec object) – tilespec from a downsampled stack

• mask_map (dict) – keys should match lowres tileids, values are mask file URI

Returns

new_highres – which highres specs are fully contained within the boundary of mask=255

Return type

List of renderapi.tilespec.TileSpec objects

asap.rough_align.apply_rough_alignment_to_montages.get_mask_paths(mask_input_dir, tilespecs, read_masks_from_lowres_stack, exts=['png', 'tif'])

asap.rough_align.do_rough_alignment module

asap.rough_align.schemas module

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

Bases: DefaultSchema

ApplyRoughAlignmentOutputParameters

key	description	default	field_type	json_type
zs	list of z values that were applied to	NA	NumpyArray	?
output_stack	stack where applied transforms were set	NA	String	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: RenderParameters

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

ApplyRoughAlignmentTransformParameters

key	description	default	field_type	json_type
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
montage_stack	stack to make a downsample version of	(REQUIRED)	String	str
prealigned_stack	stack with dropped tiles corrected for stitching errors	None	String	str
lowres_stack	montage scape stack with rough aligned transform	(REQUIRED)	String	str
output_stack	output high resolution rough aligned stack	(REQUIRED)	String	str
tilespec_directory	path to save section images	(REQUIRED)	String	str
map_z	map the montage Z indices to the rough alignment indices (default - False)	False	Boolean	bool
remap_section_ids	map section ids as well with the new z mapping. Default = False	False	Boolean	bool
consolidate_transforms	should the transforms be consolidated? (default - True)	True	Boolean	bool
scale	scale of montage scapes	(REQUIRED)	Float	float
apply_scale	do you want to apply scale	False	Boolean	bool
pool_size	pool size for parallel processing	10	Integer	int
new_z	List of new z values to be mapped to	None	List	int
old_z	List of z values to apply rough alignment to	(REQUIRED)	List	int
mask_input_dir	directory containing mask files. basenames of masks that match tileIds in the rough stack will be handled.	None	InputDir	str
read_masks_from_lowres_stack	masks will be taken from lowres tilespecs. any mask_input_dir ignored.	False	Boolean	bool
update_lowres_with_masks	should the masks be added to the rough stack?	False	Boolean	bool
filter_montage_output_with_masks	should the tiles written be filtered by the masks?	False	Boolean	bool
mask_exts	what kind of mask files to recognize	[‘png’, ‘tif’]	List	str
close_stack	whether to set output stack to COMPLETE	True	Boolean	bool

opts = <marshmallow.schema.SchemaOpts object>

validate_data(data)

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

Bases: RenderParameters

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

DownsampleMaskHandlerSchema

key	description	default	field_type	json_type
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
stack	stack that is read and modified with masks	(REQUIRED)	String	str
close_stack	set COMPLETE or not	True	Boolean	bool
mask_dir	directory containing masks, named <z>_*.png where<z> is a z value in input_stack and may be specifiedin z_apply	None	InputDir	str
collection	name of collection to be filtered by mask, or resetcan be None for no operation	None	String	str
zMask	z values for which the masks will be set	None	List	int
zReset	z values for which the masks will be reset	None	List	int
mask_exts	what kind of mask files to recognize	[‘png’, ‘tif’]	List	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

LowresStackParameters

key	description	default	field_type	json_type
stack	Input downsample images section stack	(REQUIRED)	String	str
owner	Owner of the input lowres stack	None	String	str
project	Project of the input lowres stack	None	String	str
service_host	Service host for the input stack Render service	None	String	str
baseURL	Base URL of the Render service for the source stack	None	String	str
renderbinPath	Client scripts location	None	String	str
verbose	Want the output to be verbose?	0	Integer	int

opts = <marshmallow.schema.SchemaOpts object>

class asap.rough_align.schemas.MakeAnchorStackSchema(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

MakeAnchorStackSchema

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	not used in this module, keeps parents happy	[1000]	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
transform_xml	xml transforms from trakemimages from which these are madeare assumed to be named <z>_*.png	NA	InputFile	str
transform_json	Human generated list of transforms.or, json scraped from xmlKeys are of form <z>_*.png where z matches a tilespec in input_stack and values are AffineModel transform jsonswill override xml input.	None	InputFile	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

OutputLowresStackParameters

key	description	default	field_type	json_type
stack	Input downsample images section stack	(REQUIRED)	String	str
owner	Owner of the input lowres stack	None	String	str
project	Project of the input lowres stack	None	String	str
service_host	Service host for the input stack Render service	None	String	str
baseURL	Base URL of the Render service for the source stack	None	String	str
renderbinPath	Client scripts location	None	String	str
verbose	Want the output to be verbose?	0	Integer	int

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

PairwiseRigidOutputSchema

key	description	default	field_type	json_type
minZ	minimum z value in output stack	(REQUIRED)	Integer	int
maxZ	minimum z value in output stack	(REQUIRED)	Integer	int
output_stack	name of output stack	(REQUIRED)	String	str
missing	list of z values missing in z range of output stack	(REQUIRED)	List	int
masked	list of z values masked in z range of output stack	(REQUIRED)	List	int
residuals	pairwise residuals in output stack	(REQUIRED)	List	?

opts = <marshmallow.schema.SchemaOpts object>

class asap.rough_align.schemas.PairwiseRigidSchema(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

PairwiseRigidSchema

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
match_collection	Point match collection name	(REQUIRED)	String	str
gap_file	json file {k: v} where int(k) is a z value to skipentries in here that are not already missing willbe omitted from the output stacki.e. this is a place one can skip sections	None	InputFile	str
translate_to_positive	translate output stack to positive space	True	Boolean	bool
translation_buffer	minimum (x, y) of output stack if translate_to_positive=True	[0, 0]	List	float
anchor_stack	fix transforms using tiles in this stack	None	String	str

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

PointMatchCollectionParameters

key	description	default	field_type	json_type
owner	Point match collection owner (defaults to render owner	None	String	str
match_collection	Point match collection name	(REQUIRED)	String	str
server	baseURL of the Render service holding the point match collection	None	String	str
verbose	Verbose output flag	0	Integer	int

opts = <marshmallow.schema.SchemaOpts object>

Module contents