EMaligner schema¶
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class
EMaligner.schemas.
EMA_Schema
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
argschema.schemas.ArgSchema
The input schema used by the EM_aligner_python solver
This schema is designed to be a schema_type for an ArgSchemaParser object¶ 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 first_section first section for matrix assembly (REQUIRED) Integer
int last_section last section for matrix assembly (REQUIRED) Integer
int n_parallel_jobs number of parallel jobs that will run for retrieving tilespecs, assembly from pointmatches, and import_tilespecs_parallel 4 Integer
int processing_chunk_size number of pairs per multiprocessing job. can help parallelizing pymongo calls. 1 Integer
int solve_type Solve type options (montage, 3D) montage String
str close_stack Set output stack to state COMPLETE? True Boolean
bool overwrite_zlayer delete section before import tilespecs? True Boolean
bool profile_data_load module will raise exception after timing tilespec read False Boolean
bool transformation transformation to use for the solve AffineModel String
str fullsize_transform use fullsize affine transform False Boolean
bool poly_order order of polynomial transform. 2 Integer
int output_mode none: just solve and show logging output hdf5: assemble to hdf5_options.output_dir stack: write to output stack none String
str assemble_from_file path to an hdf5 file for solving from hdf5 output.mainly for testing purposes. hdf5 output usually to be solved by external solver String
str ingest_from_file path to an hdf5 file output from the external solver. String
str render_output anything besides the default will show all the render stderr/stdout null String
str input_stack specifies the origin of the tilespecs. NA input_stack
dict output_stack specifies the destination of the tilespecs. NA output_stack
dict pointmatch specifies the origin of the point correspondences NA pointmatch
dict hdf5_options options invoked if output_mode is ‘hdf5’ NA hdf5_options
dict matrix_assembly options that control which correspondences are included in the matrix equation and their weights NA matrix_assembly
dict regularization options that contol the regularization of different types of variables in the solve NA regularization
dict transform_apply tilespec.tforms[i].tform() for i in transform_apply will be performed on the matches before matrix assembly. [] List
int -
opts
= <marshmallow.schema.SchemaOpts object>¶
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validate_data
(data)¶
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class
EMaligner.schemas.
input_stack
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
EMaligner.schemas.input_db
¶ key description default field_type json_type owner render or mongo owner String
str project render or mongo project String
str name render or mongo collection name NA List
str host render host NA String
str port render port 8080 Integer
int mongo_host mongodb host em-131fs String
str mongo_port mongodb port 27017 Integer
int mongo_userName mongo user name String
str mongo_authenticationDatabase mongo admin db String
str mongo_password mongo pwd String
str db_interface render: read or write via render mongo: read or write via pymongo file: read or write to file mongo String
str client_scripts see renderapi.render.RenderClient /allen/aibs/pipeline/image_processing/volume_assembly/render-jars/production/scripts String
str memGB see renderapi.render.RenderClient 5G String
str validate_client see renderapi.render.RenderClient False Boolean
bool input_file json or json.gz serialization of input None InputFile
str collection_type ‘stack’ or ‘pointmatch’ stack String
str use_rest passed as arg in import_tilespecs_parallel False Boolean
bool -
opts
= <marshmallow.schema.SchemaOpts object>¶
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validate_data
(data)¶
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class
EMaligner.schemas.
output_stack
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
EMaligner.schemas.db_params
¶ key description default field_type json_type owner render or mongo owner String
str project render or mongo project String
str name render or mongo collection name NA List
str host render host NA String
str port render port 8080 Integer
int mongo_host mongodb host em-131fs String
str mongo_port mongodb port 27017 Integer
int mongo_userName mongo user name String
str mongo_authenticationDatabase mongo admin db String
str mongo_password mongo pwd String
str db_interface render: read or write via render mongo: read or write via pymongo file: read or write to file mongo String
str client_scripts see renderapi.render.RenderClient /allen/aibs/pipeline/image_processing/volume_assembly/render-jars/production/scripts String
str memGB see renderapi.render.RenderClient 5G String
str validate_client see renderapi.render.RenderClient False Boolean
bool output_file json or json.gz serialization of input stackResolvedTiles. None OutputFile
str compress_output if writing file, compress with gzip. True Boolean
bool collection_type ‘stack’ or ‘pointmatch’ stack String
str use_rest passed as kwarg to renderapi.client.import_tilespecs_parallel False Boolean
bool -
opts
= <marshmallow.schema.SchemaOpts object>¶
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validate_data
(data)¶
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validate_file
(data)¶
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class
EMaligner.schemas.
pointmatch
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
EMaligner.schemas.input_db
¶ key description default field_type json_type owner render or mongo owner String
str project render or mongo project String
str name render or mongo collection name NA List
str host render host NA String
str port render port 8080 Integer
int mongo_host mongodb host em-131fs String
str mongo_port mongodb port 27017 Integer
int mongo_userName mongo user name String
str mongo_authenticationDatabase mongo admin db String
str mongo_password mongo pwd String
str db_interface render: read or write via render mongo: read or write via pymongo file: read or write to file mongo String
str client_scripts see renderapi.render.RenderClient /allen/aibs/pipeline/image_processing/volume_assembly/render-jars/production/scripts String
str memGB see renderapi.render.RenderClient 5G String
str validate_client see renderapi.render.RenderClient False Boolean
bool input_file json or json.gz serialization of input None InputFile
str collection_type ‘stack’ or ‘pointmatch’ pointmatch String
str -
opts
= <marshmallow.schema.SchemaOpts object>¶
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class
EMaligner.schemas.
hdf5_options
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
argschema.schemas.DefaultSchema
¶ key description default field_type json_type output_dir path to directory to hold hdf5 output. String
str chunks_per_file how many sections with upward-looking cross section to write per .h5 file 5 Integer
int -
opts
= <marshmallow.schema.SchemaOpts object>¶
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class
EMaligner.schemas.
matrix_assembly
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
argschema.schemas.DefaultSchema
¶ key description default field_type json_type depth depth in z for matrix assembly point matches [0, 1, 2] List
int explicit_weight_by_depth explicitly set solver weights by depth None List
float cross_pt_weight weight of cross section point matches 1.0 Float
float montage_pt_weight weight of montage point matches 1.0 Float
float npts_min disregard any tile pairs with fewer points than this 5 Integer
int npts_max truncate any tile pairs to this size 500 Integer
int choose_random choose random pts to meet npts_max vs. just first npts_max False Boolean
bool inverse_dz cross section point match weighting fades with z True Boolean
bool -
check_explicit
(data)¶
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opts
= <marshmallow.schema.SchemaOpts object>¶
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tolist
(data)¶
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class
EMaligner.schemas.
regularization
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
argschema.schemas.DefaultSchema
¶ key description default field_type json_type default_lambda common regularization value 0.005 Float
float translation_factor translation regularization factor. multiplies default_lambda 0.005 Float
float poly_factors List of regularization factors by order (0, 1, …, n) will override other settings for Polynomial2DTransform. multiplies default_lambda None List
float thinplate_factor regularization factor for thin plate spline control points. multiplies default_lambda. 1e-05 Float
float -
opts
= <marshmallow.schema.SchemaOpts object>¶
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class
EMaligner.schemas.
EMA_PlotSchema
(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)¶ Bases:
EMaligner.schemas.EMA_Schema
This schema is designed to be a schema_type for an ArgSchemaParser object¶ 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 first_section first section for matrix assembly (REQUIRED) Integer
int last_section last section for matrix assembly (REQUIRED) Integer
int n_parallel_jobs number of parallel jobs that will run for retrieving tilespecs, assembly from pointmatches, and import_tilespecs_parallel 4 Integer
int processing_chunk_size number of pairs per multiprocessing job. can help parallelizing pymongo calls. 1 Integer
int solve_type Solve type options (montage, 3D) montage String
str close_stack Set output stack to state COMPLETE? True Boolean
bool overwrite_zlayer delete section before import tilespecs? True Boolean
bool profile_data_load module will raise exception after timing tilespec read False Boolean
bool transformation transformation to use for the solve AffineModel String
str fullsize_transform use fullsize affine transform False Boolean
bool poly_order order of polynomial transform. 2 Integer
int output_mode none: just solve and show logging output hdf5: assemble to hdf5_options.output_dir stack: write to output stack none String
str assemble_from_file path to an hdf5 file for solving from hdf5 output.mainly for testing purposes. hdf5 output usually to be solved by external solver String
str ingest_from_file path to an hdf5 file output from the external solver. String
str render_output anything besides the default will show all the render stderr/stdout null String
str input_stack specifies the origin of the tilespecs. NA input_stack
dict output_stack specifies the destination of the tilespecs. NA output_stack
dict pointmatch specifies the origin of the point correspondences NA pointmatch
dict hdf5_options options invoked if output_mode is ‘hdf5’ NA hdf5_options
dict matrix_assembly options that control which correspondences are included in the matrix equation and their weights NA matrix_assembly
dict regularization options that contol the regularization of different types of variables in the solve NA regularization
dict transform_apply tilespec.tforms[i].tform() for i in transform_apply will be performed on the matches before matrix assembly. [] List
int z1 first z for plot 1000 Integer
int z2 second z for plot 1000 Integer
int zoff z offset between pointmatches and tilespecs 0 Integer
int plot make a plot, otherwise, just text output True Boolean
bool savefig save to a pdf False Boolean
bool plot_dir no description ./ String
str threshold threshold for colors in residual plot [pixels] 5.0 Float
float density whether residual plot is density (for large numbers of points) or just points True Boolean
bool -
opts
= <marshmallow.schema.SchemaOpts object>¶
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