asap.em_montage_qc package

Submodules

asap.em_montage_qc.detect_montage_defects module

asap.em_montage_qc.plots module

asap.em_montage_qc.schemas module

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)[source]

Bases: asap.module.schemas.schemas.RenderParameters, asap.module.schemas.stack_schemas.ZValueParameters, asap.module.schemas.stack_schemas.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
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)[source]

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)[source]

Bases: argschema.schemas.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`	?

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)[source]