asap.em_montage_qc package

Submodules

asap.em_montage_qc.detect_montage_defects module

class asap.em_montage_qc.detect_montage_defects.DetectMontageDefectsModule(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 DetectMontageDefectsParameters

default_output_schema

alias of DetectMontageDefectsParametersOutput

default_schema

alias of DetectMontageDefectsParameters

run()

asap.em_montage_qc.detect_montage_defects.check_status_of_stack(render, stack, zvalues)

asap.em_montage_qc.detect_montage_defects.detect_disconnected_tiles(render, prestitched_stack, poststitched_stack, z, pre_tilespecs=None, post_tilespecs=None)

asap.em_montage_qc.detect_montage_defects.detect_distortion(render, poststitched_stack, zvalue, threshold_cutoff=[0.005, 0.005], pool_size=20)

asap.em_montage_qc.detect_montage_defects.detect_seams(render, stack, match_collection, match_owner, z, residual_threshold=8, distance=60, min_cluster_size=15, tspecs=None)

asap.em_montage_qc.detect_montage_defects.detect_stitching_gaps(render, prestitched_stack, poststitched_stack, z, pre_tilespecs=None, tilespecs=None)

asap.em_montage_qc.detect_montage_defects.detect_stitching_mistakes(render, prestitched_stack, poststitched_stack, match_collection, match_collection_owner, threshold_cutoff, residual_threshold, neighbor_distance, min_cluster_size, zvalues, pool_size=20)

asap.em_montage_qc.detect_montage_defects.get_pre_post_tspecs(render, prestitched_stack, poststitched_stack, z)

asap.em_montage_qc.detect_montage_defects.run_analysis(render, prestitched_stack, poststitched_stack, match_collection, match_collection_owner, residual_threshold, neighbor_distance, min_cluster_size, threshold_cutoff, z)

asap.em_montage_qc.plots module

asap.em_montage_qc.plots.plot_defects(render, stack, out_html_dir, args)

asap.em_montage_qc.plots.plot_residual(xs, ys, residual)

asap.em_montage_qc.plots.plot_section_maps(render, stack, post_tspecs, matches, disconnected_tiles, gap_tiles, seam_centroids, stats, zvalues, out_html_dir=None, pool_size=5)

asap.em_montage_qc.plots.point_match_plot(tilespecsA, matches, tilespecsB=None)

asap.em_montage_qc.schemas module

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

Bases: RenderParameters, ZValueParameters, ProcessPoolParameters

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

DetectDistortionParameters

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_stacks	List of input stacks	None	List	str
threshold_cutoff	Threshold for MAD cutoff in x and y	[0.005, 0.005]	List	float

input_stacks

match_collections = argschema.fields.List(

argschema.fields.Str, required=True, description=’List of montage point match collections’)

match_collection_owners = argschema.fields.List(

argschema.fields.Str, required=False, default=None, missing=None, description=’List of the match collection owners’)

opts = <marshmallow.schema.SchemaOpts object>

threshold_cutoff

num_threads = argschema.fields.Int(

required=False, default=20, description=’Number of parallel threads’)

@post_load def add_match_collection_owner(self, data):

if data[‘match_collection_owners’] is None:

data[‘match_collection_owners’] = [data[‘render’][‘owner’]] * len(data[‘match_collections’])

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

Bases: DefaultSchema

DetectDistortionParametersOutput

key	description	default	field_type	json_type
distorted_sections	List of sections that are distorted	(REQUIRED)	List	int

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: RenderParameters, ZValueParameters, ProcessPoolParameters

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

DetectMontageDefectsParameters

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
prestitched_stack	Pre stitched stack (raw stack)	(REQUIRED)	String	str
poststitched_stack	Stitched montage stack	(REQUIRED)	String	str
match_collection	Name of the montage point match collection	NA	String	str
match_collection_owner	Name of the match collection owner	None	String	str
residual_threshold	threshold value to filter residuals for detecting seams (default = 4)	4	Integer	int
neighbors_distance	distance in pixels to look for neighboring points in seam detection (default = 60)	80	Integer	int
min_cluster_size	minimum number of point matches required in each cluster for taking it into account for seam detection (default = 7)	12	Integer	int
threshold_cutoff	Threshold for MAD cutoff in x and y	[0.005, 0.005]	List	float
plot_sections	Do you want to plot the sections with defects (holes or gaps)?. Will plot Bokeh plots in a html file	True	Boolean	bool
out_html_dir	Folder to save the Bokeh plot defaults to /tmp directory	None	InputDir	str

add_match_collection_owner(data)

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

DetectMontageDefectsParametersOutput

key	description	default	field_type	json_type
output_html	Output html file with Bokeh plots showing holes and stitching gaps	None	List	str
qc_passed_sections	List of sections that passed QC	(REQUIRED)	List	int
hole_sections	List of z values which failed QC and has holes	(REQUIRED)	List	int
gap_sections	List of z values which have stitching gaps	(REQUIRED)	List	int
seam_sections	List of z values which have seams detected	(REQUIRED)	List	int
seam_centroids	An array of (x,y) positions of seams for each section with seams	(REQUIRED)	NumpyArray	?
distorted_sections	List of sections that are distorted	(REQUIRED)	List	int

opts = <marshmallow.schema.SchemaOpts object>

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

Bases: DefaultSchema

RoughQCOutputSchema

key	description	default	field_type	json_type
iou_plot	Pdf/html file showing IOU plots	(REQUIRED)	OutputFile	str
distortion_plot	Pdf/html file with distortion plots	(REQUIRED)	OutputFile	str

opts = <marshmallow.schema.SchemaOpts object>

class asap.em_montage_qc.schemas.RoughQCSchema(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

RoughQCSchema

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
input_downsampled_stack	Pre rough aligned downsampled stack	(REQUIRED)	String	str
output_downsampled_stack	Rough aligned stack name	(REQUIRED)	String	str
minZ	min z	(REQUIRED)	Integer	int
maxZ	max z	(REQUIRED)	Integer	int
pool_size	Pool size	10	Integer	int
output_dir	temp filename to save fig	None	OutputDir	str
out_file_format	Do you want the output to be bokeh plots in html (option = ‘html’) or pdf files for plots (option = ‘pdf’, default)	pdf	String	str

opts = <marshmallow.schema.SchemaOpts object>

Module contents