tmclient package¶

Submodules¶

tmclient.base module¶

class tmclient.base.HttpClient(host, port, username, password, ca_bundle=None)¶

Bases: object

Abstract base class for HTTP client interface.

Parameters:

host: str

name of the TissueMAPS host

port: int

number of the port to which TissueMAPS server listens

username: str

name of the TissueMAPS user

password: str

password for username

ca_bundle: str, optional

path to a CA bundle file in Privacy Enhanced Mail (PEM) format; only used with HTTPS when port is set to 443

tmclient.api module¶

class tmclient.api.TmClient(host, port, username, password, experiment_name=None, ca_bundle=None)¶

Bases: tmclient.base.HttpClient

TissueMAPS RESTful API client.

Parameters:

host: str

name or IP address of the machine that hosts the TissueMAPS server (e.g. "localhost", 127.0.0.1 or app.tissuemaps.org)

port: int

number of the port to which server listens (e.g. 80, 443 or 8002)

username: str

name of the TissueMAPS user

password: str

password for the user (can also be provided via the tm_pass file)

experiment_name: str, optional

name of the experiment that should be accessed

ca_bundle: str, optional

path to a CA bundle file in Privacy Enhanced Mail (PEM) format

Examples

# Access general resources >>>client = TmClient(‘localhost’, 8002, ‘devuser’, ‘123456’) >>>client.get_experiments()

# Access experiment-specific resources, exemplied for an experiment # called “test”. # The name of the experiment can be provided via the constructor: >>>client = TmClient(‘localhost’, 8002, ‘devuser’, ‘123456’, ‘test’) >>>client.get_plates() # Alternatively, it can be set separately: >>>client = TmClient(‘localhost’, 8002, ‘devuser’, ‘123456’) >>>client.experiment_name = ‘test’ >>>client.get_plates()

create_acquisition(plate_name, name, description='')¶

Creates a new acquisition.

Parameters:

plate_name: str

name of the parent plate

name: str

name that should be given to the acquisition

description: str, optional

description of the acquisition

Returns:

dict

acquisition resource representation

create_experiment(workflow_type, microscope_type, plate_format, plate_acquisition_mode)¶

Creates the experiment.

Parameters:

workflow_type: str

workflow type

microscope_type: str

microscope type

plate_format: int

well-plate format, i.e. total number of wells per plate

plate_acquisition_mode: str

mode of image acquisition that determines whether acquisitions will be interpreted as time points as part of a time series experiment or as multiplexing cycles as part of a serial multiplexing experiment

Returns:

dict

experiment resource representation

create_mapobject_type(name)¶

Creates a mapobject type.

Parameters:

name: str

name that should be given to the mapobject type

create_plate(name, description='')¶

Creates a new plate.

Parameters:

name: str

name that should be given to the plate

description: str, optional

description of the plate

Returns:

dict

plate resource representation

delete_acquisition(plate_name, name)¶

Deletes an acquisition.

Parameters:

plate_name: str

name of the parent plate

name: str

name of the acquisition that should be deleted

delete_experiment()¶: Deletes the experiment.

See also

tmserver.api.experiment.delete_experiment(), tmlib.models.experiment.ExperimentReference, tmlib.models.experiment.Experiment

delete_feature(mapobject_type_name, name)¶

Deletes a feature.

Parameters:

mapobject_type_name: str

name of the segmented objects type

name: str

name of the feature that should be renamed

delete_mapobject_type(name)¶

Deletes a mapobject type.

Parameters:

name: str

name of the mapobject type that should be renamed

delete_plate(name)¶

Deletes a plate.

Parameters:

name: str

name of the plate that should be deleted

download_channel_image(channel_name, plate_name, well_name, well_pos_y, well_pos_x, cycle_index=0, tpoint=0, zplane=0, correct=True)¶

Downloads a channel image.

Parameters:

channel_name: str

name of the channel

plate_name: str

name of the plate

well_name: str

name of the well

well_pos_x: int

zero-based x cooridinate of the acquisition site within the well

well_pos_y: int

zero-based y cooridinate of the acquisition site within the well

cycle_index: str, optional

zero-based cycle index (default: 0)

tpoint: int, optional

zero-based time point index (default: 0)

zplane: int, optional

zero-based z-plane index (default: 0)

correct: bool, optional

whether image should be corrected for illumination artifacts (default: True)

Returns:

numpy.ndarray[numpy.uint16 or numpy.uint8]

pixel/voxel array and filename

download_channel_image_file(channel_name, plate_name, well_name, well_pos_y, well_pos_x, cycle_index, tpoint, zplane, correct, directory)¶

Downloads a channel image and writes it to a PNG file on disk.

Parameters:

channel_name: str

name of the channel

plate_name: str

name of the plate

well_name: str

name of the well

well_pos_x: int

zero-based x cooridinate of the acquisition site within the well

well_pos_y: int

zero-based y cooridinate of the acquisition site within the well

cycle_index: str

zero-based cycle index

tpoint: int

zero-based time point index

zplane: int

zero-based z-plane index

correct: bool

whether image should be corrected for illumination artifacts

directory: str

absolute path to the directory on disk where the file should be saved

download_feature_values(mapobject_type_name, plate_name=None, well_name=None, well_pos_y=None, well_pos_x=None, tpoint=None)¶

Downloads feature values for the given MapobjectType.

Parameters:

mapobject_type_name: str

type of the segmented objects

plate_name: str, optional

name of the plate

well_name: str, optional

name of the well

well_pos_y: int, optional

y-position of the site relative to the well grid

well_pos_x: int, optional

x-position of the site relative to the well grid

tpoint: int, optional

zero-based time point index

Returns:

pandas.DataFrame

n*x*p dataframe, where n are number of objects and p number of features

download_feature_values_and_metadata_files(mapobject_type_name, directory, parallel=1)¶

Downloads all feature values for the given object type and stores the data as CSV files on disk.

Parameters:

mapobject_type_name: str

type of the segmented objects

directory: str

absolute path to the directory on disk where the file should be

parallel: int

number of parallel processes to use for upload

download_jterator_project()¶

Downloads the jterator project.

Returns:

dict

“pipeline” description and a “handles” descriptions for each module in the pipeline

download_jterator_project_files(directory)¶

Downloads the jterator project and stores it on disk in YAML format. The pipeline description will be stored in a pipeline.yaml file in directory and each handle description will be stored in a *handles.yaml file and placed into a handles subfolder of directory.

Parameters:

directory: str

path to the root folder where files should be stored

download_object_metadata(mapobject_type_name, plate_name=None, well_name=None, well_pos_y=None, well_pos_x=None, tpoint=None)¶

Downloads metadata for the given object type, which describes the position of each segmented object on the map.

Parameters:

mapobject_type_name: str

type of the segmented objects

plate_name: str, optional

name of the plate

well_name: str, optional

name of the well

well_pos_y: int, optional

y-position of the site relative to the well grid

well_pos_x: int, optional

x-position of the site relative to the well grid

tpoint: int, optional

zero-based time point index

Returns:

pandas.DataFrame

n*x*p dataframe, where n are number of objects and p number of metadata attributes

See also

tmserver.api.feature.get_metadata()

download_segmentation_image(mapobject_type_name, plate_name, well_name, well_pos_y, well_pos_x, tpoint=0, zplane=0)¶

Downloads a segmentation image.

Parameters:

plate_id: int

ID of the parent experiment

mapobject_type_name: str

name of the segmented objects

plate_name: str

name of the plate

well_name: str

name of the well in which the image is located

well_pos_y: int

y-position of the site relative to the well grid

well_pos_x: int

x-position of the site relative to the well grid

tpoint: int, optional

zero-based time point index (default: 0)

zplane: int, optional

zero-based z-plane index (default: 0)

Returns:

numpy.ndarray[numpy.int32]

labeled image where each label encodes a segmented object

See also

tmserver.api.mapobject.download_segmentations(), tmlib.models.mapobject.MapobjectSegmentation

download_segmentation_image_file(mapobject_type_name, plate_name, well_name, well_pos_y, well_pos_x, tpoint, zplane, directory)¶

Downloads a segmentation image and writes it to a PNG file on disk.

Parameters:

mapobject_type_name: str

name of the segmented objects

plate_name: str

name of the plate

well_name: str

name of the well in which the image is located

well_pos_y: int

y-position of the site relative to the well grid

well_pos_x: int

x-position of the site relative to the well grid

tpoint: int

zero-based time point index

zplane: int

zero-based z-plane index

directory: str

absolute path to the directory on disk where the file should be saved

download_workflow_description()¶

Downloads the workflow description. In case no description has been uploaded so far, the server sends a default template.

Returns:

dict

workflow description

download_workflow_description_file(filename)¶

Downloads the workflow description and writes it to a YAML file.

Parameters:

filename: str

path to the file to which description should be written

experiment_name¶: str: name of the currently accessed experiment

get_acquisitions(plate_name=None)¶

Gets information about acquisitions.

Parameters:

plate_name: str, optional

name of the parent plate for which acquisitions should be filtered

Returns:

List[Dict[str, str]]

id, name, status, description and plate_name for each acquisition

get_channels()¶

Gets channels.

Returns:

List[Dict[str, str]]

information about each channel

get_cycles()¶

Gets cycles.

Returns:

List[Dict[str, str]]

information about each cycle

See also

tmserver.api.cycle.get_cycles(), tmlib.models.cycles.Cycle

get_experiments()¶

Gets information for all experiments.

Returns:

List[Dict[str, str]]

id, name and description for each experiment

get_features(mapobject_type_name)¶

Gets features for a given object type.

Parameters:

mapobject_type_name: str

type of the segmented objects

Returns:

List[Dict[str, str]]

information about each feature

See also

tmserver.api.feature.get_features(), tmlib.models.feature.Feature

get_mapobject_types()¶

Gets object types.

Returns:

List[Dict[str, str]]

inforamation about each mapobject type

get_microscope_files(plate_name, acquisition_name)¶

Gets status and name of files that have been registered for upload.

Parameters:

plate_name: str

name of the parent plate

acquisition_name: str

name of the parent acquisition

Returns:

List[Dict[str, str]]

names and status of uploaded files

get_plates()¶

Gets information about plates.

Returns:

List[Dict[str, str]]

id, name, status and description for each plate

get_sites(plate_name=None, well_name=None)¶

Gets information about sites.

Parameters:

plate_name: str, optional

name of the parent plate for which sites should be filtered

well_name: str, optional

name of the parent well for which sites should be filtered

Returns:

List[Dict[str, str]]

id, name and description of each well

get_tool_results()¶

Gets tool results.

Returns:

List[Dict[str, str]]

information about each tool result

See also

tmserver.api.tools.get_tool_results(), tmlib.models.result.ToolResult

get_tools_status(tool_name=None)¶

Gets the status of tool jobs.

Parameters:

tool_name: str, optional

filter jobs by tool name

Returns:

dict

status information about tool jobs

See also

tmserver.api.tools.get_tools_status(), tmlib.workflow.utils.get_task_status(), tmlib.models.submission.Task

get_wells(plate_name=None)¶

Gets information about wells.

Parameters:

plate_name: str, optional

name of the parent plate

Returns:

List[Dict[str, str]]

id, name and description of each well

get_workflow_status(depth=2)¶

Gets the workflow status.

Parameters:

depth: int, optional

query depth - in which detail status of subtasks will be queried

Returns:

dict

status information about the workflow

See also

tmserver.api.workflow.get_workflow_status(), tmlib.workflow.utils.get_task_status(), tmlib.models.submission.Task

kill_workflow()¶: Kills the workflow.

See also

tmserver.api.workflow.kill_workflow(), tmlib.workflow.workflow.Workflow

rename_acquisition(plate_name, name, new_name)¶

Renames an acquisition.

Parameters:

plate_name: str

name of the parent plate

name: str

name of the acquisition that should be renamed

new_name: str

name that should be given to the acquisition

rename_channel(name, new_name)¶

Renames a channel.

Parameters:

name: str

name of the channel that should be renamed

new_name: str

name that should be given to the channel

rename_experiment(new_name)¶: Renames the experiment.

See also

tmserver.api.experiment.update_experiment(), tmlib.models.experiment.ExperimentReference

rename_feature(mapobject_type_name, name, new_name)¶

Renames a feature.

Parameters:

mapobject_type_name: str

name of the segmented objects type

name: str

name of the feature that should be renamed

new_name: str

name that should be given to the feature

rename_mapobject_type(name, new_name)¶

Renames a mapobject type.

Parameters:

name: str

name of the mapobject type that should be renamed

new_name: str

name that should be given to the mapobject type

rename_plate(name, new_name)¶

Renames a plate.

Parameters:

name: str

name of the plate that should be renamed

new_name: str

name that should be given to the plate

resubmit_workflow(stage_name=None, description=None)¶

Resubmits the workflow.

Parameters:

stage_name: str, optional

name of the stage at which workflow should be resubmitted (when omitted workflow will be restarted from the beginning)

description: dict, optional

workflow description

submit_workflow(description=None)¶

Submits the workflow.

Parameters:

description: dict, optional

workflow description

upload_feature_values(mapobject_type_name, plate_name, well_name, well_pos_y, well_pos_x, tpoint, data)¶

Uploads feature values for the given MapobjectType at the specified Site.

Parameters:

mapobject_type_name: str

type of the segmented objects

plate_name: str

name of the plate

well_name: str

name of the well

well_pos_y: int

y-position of the site relative to the well grid

well_pos_x: int

x-position of the site relative to the well grid

tpoint: int

zero-based time point index

data: pandas.DataFrame

n*x*p dataframe, where n are number of objects at this site and p number of features (index must be site-specific one-based labels that must match those of the corresponding segmentation image)

upload_jterator_project(pipeline, handles)¶

Uploads a jterator project.

Parameters:

pipeline: dict

description of the jterator pipeline

handles: dict, optional

description of each module in the jterator pipeline

See also

tmserver.api.workflow.update_jterator_project(), tmlib.workflow.jterator.description.PipelineDescription, tmlib.workflow.jterator.description.HandleDescriptions

upload_jterator_project_files(directory)¶

Uploads the jterator project description from files on disk in YAML format. It expects a pipeline.yaml file in directory and optionally *handles.yaml files in a handles subfolder of directory.

Parameters:

directory: str

path to the root folder where files are located

upload_microscope_files(plate_name, acquisition_name, directory, parallel=1, retry=5)¶

Uploads microscope files contained in directory.

Parameters:

plate_name: str

name of the parent plate

acquisition_name: str

name of the parent acquisition

directory: int

path to a directory on disk where the files that should be uploaded are located

parallel: int

number of parallel processes to use for upload

Returns:

List[str]

names of registered files

See also

tmserver.api.acquisition.add_microscope_file(), tmlib.models.file.MicroscopeImageFile, tmlib.models.file.MicroscopeMetadataFile

upload_segmentation_image(mapobject_type_name, plate_name, well_name, well_pos_y, well_pos_x, tpoint, zplane, image)¶

Uploads a segmentation image.

Parameters:

mapobject_type_name: str

name of the segmented objects

plate_name: str

name of the plate

well_name: str

name of the well in which the image is located

well_pos_y: int

y-position of the site relative to the well grid

well_pos_x: int

x-position of the site relative to the well grid

tpoint: int, optional

zero-based time point index (default: 0)

zplane: int, optional

zero-based z-plane index (default: 0)

image: numpy.ndarray[numpy.int32]

labeled array

Raises:

TypeError

when image is not provided in form of a numpy array

ValueError

when image doesn’t have 32-bit unsigned integer data type

upload_segmentation_image_file(mapobject_type_name, plate_name, well_name, well_pos_y, well_pos_x, tpoint, zplane, filename)¶

Uploads segmentations from a PNG image file.

Parameters:

mapobject_type_name: str

name of the segmented objects

plate_name: str

name of the plate

well_name: str

name of the well in which the image is located

well_pos_y: int

y-position of the site relative to the well grid

well_pos_x: int

x-position of the site relative to the well grid

tpoint: int, optional

zero-based time point index (default: 0)

zplane: int, optional

zero-based z-plane index (default: 0)

filename: str

path to the file on disk

upload_workflow_description(description)¶

Uploads a workflow description.

Parameters:

dict

workflow description

upload_workflow_description_file(filename)¶

Uploads workflow description from a YAML file.

Parameters:

filename: str

path to the file from which description should be read

tm_client¶

TissueMAPS REST API client (version: 0.3.3).

-h, --help¶: show this help message and exit

-H <host>, --host <host>¶: name of TissueMAPS server host

-P <port>, --port <port>¶: number of the port to which the server listens (default: 80)

-u <username>, --user <username>¶: name of TissueMAPS user

-p <password>, --password <password>¶: password of TissueMAPS user

-v, --verbosity¶: increase logging verbosity

tm_client acquisition¶

Access acquisition resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client acquisition create¶

Create a new acquisition for an existing plate.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

-p <plate>, --plate <plate>¶: name of the plate

--description <description>¶: optional description

tm_client acquisition ls¶

List acquisitions.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of a plate

tm_client acquisition rename¶

Rename an acquisition.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

-p <plate>, --plate <plate>¶: name of the plate

--new-name <new_name>¶: new name

tm_client acquisition rm¶

Delete an acquisition.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

-p <plate>, --plate <plate>¶: name of the plate

tm_client channel¶

Access channel resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client channel ls¶

List channels.

-h, --help¶: show this help message and exit

tm_client channel rename¶

Rename a channel.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

--new-name <new_name>¶: new name

tm_client channel-image¶

Access channel image resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client channel-image download¶

Download channel image to PNG file.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of the plate

-w <well>, --well <well>¶: name of the well

-x <x>, --well-pos-x <x>¶: zero-based x cooridinate of acquisition site within the well

-y <y>, --well-pos-y <y>¶: zero-based y cooridinate of acquisition site within the well

-t <t>, --tpoint <t>¶: zero-based time point index

-z <z>, --zplane <z>¶: zero-based z-plane index

-c <c>, --channel <c>¶: name of the channel

--directory <directory>¶: directory where download should be stored (defaults to temporary directory)

-i <cycle_index>, --cycle-index <cycle_index>¶: zero-based index of the cycle

--correct¶: whether image should be corrected for illumination artifacts

tm_client experiment¶

Access experiment resources.

-h, --help¶: show this help message and exit

tm_client experiment create¶

Create the experiment.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

--workflow-type <workflow_type>¶: workflow type (default: canonical)

--microscope-type <microscope_type>¶: microscope type (default: cellvoyager)

--plate-format <plate_format>¶: well-plate format, i.e. total number of wells per plate (default: 384)

--plate-acquisition-mode {multiplexing,basic}¶: whether multiple acquisitions of the same plate are interpreted as time points (“basic” mode) or multiplexing cycles (“multiplexing” mode) (default: basic)

tm_client experiment ls¶

List experiments.

-h, --help¶: show this help message and exit

tm_client experiment rename¶

Rename the experiment.

-h, --help¶: show this help message and exit

--new-name <new_name>¶: new name

-n <name>, --name <name>¶: name

tm_client experiment rm¶

Delete the experiment.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

tm_client feature¶

Access feature resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client feature ls¶

List features for a given object type.

-h, --help¶: show this help message and exit

-o <object-type>, --object-type <object-type>¶: name of the objects type

tm_client feature rename¶

Rename a feature.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

-o <object-type>, --object-type <object-type>¶: name of the objects type

--new-name <new_name>¶: new name

tm_client feature rm¶

Delete a feature.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

-o <object-type>, --object-type <object-type>¶: name of the objects type

tm_client feature-values¶

Access feature values resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client feature-values download¶

Download feature values for segmented objects as well as the corresponding metadata.

-h, --help¶: show this help message and exit

-o <object-type>, --object-type <object-type>¶: name of the objects type

--directory <directory>¶: directory where download should be stored (defaults to temporary directory)

--parallel <num>¶: Use NUM parallel processes for download (default: 1). If NUM is omitted or 0, the degree of parallelism is proportional to the number of available CPUs.

tm_client jtproject¶

Access jterator project resources. A jterator project consists of a pipeline descriptor file in YAML format and additional module descriptor files (handles) in YAML format. A project is represented on disk as a folder containing a “pipeline.yaml” file and a “handles” subfolder containing any “*.handles.yaml” files.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client jtproject download¶

Download the project description.

-h, --help¶: show this help message and exit

--directory <directory>¶: directory where download should be stored (defaults to temporary directory)

tm_client jtproject upload¶

Upload a project, updating any potentially existing project.

-h, --help¶: show this help message and exit

--directory <directory>¶: path to directory from which project should be read

tm_client microscope-file¶

Access microscope file resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client microscope-file ls¶

List microscope files.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of the plate

-a <acquisition>, --acquisition <acquisition>¶: name of the acquisition

tm_client microscope-file upload¶

Upload microscope image and metadata files.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of the plate

-a <acquisition>, --acquisition <acquisition>¶: name of the acquisition

--directory <directory>¶: path to directory where files are located

--parallel <num>¶: Use NUM parallel processes for upload (default: 1). If NUM is omitted or 0, the degree of parallelism is proportional to the number of available CPUs.

--retries <num>¶: Retry failed uploads up to NUM times. If this option is omitted, tm_client will retry failed uploads up to 5 times.

--no-retry¶: Do not retry failed uploads.

tm_client object-type¶

Access object type resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client object-type create¶

Create a new object type.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

tm_client object-type ls¶

List object types.

-h, --help¶: show this help message and exit

tm_client object-type rename¶

Rename an object type.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

--new-name <new_name>¶: new name

tm_client object-type rm¶

Delete an objects type.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

tm_client plate¶

Access plate resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client plate create¶

Create a new plate.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

--description <description>¶: optional description

tm_client plate ls¶

List plates.

-h, --help¶: show this help message and exit

tm_client plate rename¶

Rename a plate.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

--new-name <new_name>¶: new name

tm_client plate rm¶

Delete a plate.

-h, --help¶: show this help message and exit

-n <name>, --name <name>¶: name

tm_client segmentation¶

Access segmentation resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client segmentation download¶

Download segmentations in form of a 16-bit PNG image file. WARNING: This approach only works when the image contains less than 65536 objects.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of the plate

-w <well>, --well <well>¶: name of the well

-x <x>, --well-pos-x <x>¶: zero-based x cooridinate of acquisition site within the well

-y <y>, --well-pos-y <y>¶: zero-based y cooridinate of acquisition site within the well

-t <t>, --tpoint <t>¶: zero-based time point index

-z <z>, --zplane <z>¶: zero-based z-plane index

-o <object-type>, --object-type <object-type>¶: name of the objects type

--directory <directory>¶: directory where download should be stored (defaults to temporary directory)

tm_client segmentation upload¶

Upload object segmentations in from of a 16-bit PNG image file. The image must be labeled such that background pixels have zero values and pixels within objects have unsigned integer values. WARNING: This approach only works when the image contains less than 65536 objects.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of the plate

-w <well>, --well <well>¶: name of the well

-x <x>, --well-pos-x <x>¶: zero-based x cooridinate of acquisition site within the well

-y <y>, --well-pos-y <y>¶: zero-based y cooridinate of acquisition site within the well

-t <t>, --tpoint <t>¶: zero-based time point index

-z <z>, --zplane <z>¶: zero-based z-plane index

-o <object-type>, --object-type <object-type>¶: name of the objects type

--filename <filename>¶: path to the file on disk

tm_client site¶

Access site resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client site ls¶

List sites.

-h, --help¶: show this help message and exit

tm_client tools¶

Access tools resources of the experiment.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client tools log¶

Show the log output of tool job.

-h, --help¶: show this help message and exit

--name <name>¶: name of the job

--submission <submission_id>¶: number of the submission

tm_client tools ls¶

List available tool results.

-h, --help¶: show this help message and exit

tm_client tools status¶

Show the status of tool jobs.

-h, --help¶: show this help message and exit

--tool <tool_name>¶: filter jobs by tool name

tm_client well¶

Access well resources.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client well ls¶

List wells.

-h, --help¶: show this help message and exit

-p <plate>, --plate <plate>¶: name of a plate

tm_client workflow¶

Access workflow resources of the experiment.

-h, --help¶: show this help message and exit

-e <experiment>, --experiment <experiment>¶: name of the experiment

tm_client workflow download¶

Download the workflow description.

-h, --help¶: show this help message and exit

--file <filename>¶: path to YAML file to which workflow description should be written

tm_client workflow kill¶

Kill the workflow.

-h, --help¶: show this help message and exit

tm_client workflow log¶

Show the log output of an individual job.

-h, --help¶: show this help message and exit

-s <step_name>, --step <step_name>¶: name of the workflow step

-n <name>, --name <name>¶: name of the job

tm_client workflow resubmit¶

Resubmit the workflow at the given stage using a previoulsy uploaded description.

-h, --help¶: show this help message and exit

-s <stage_name>, --stage <stage_name>¶: name of the stage at which the workflow should be resubmitted

tm_client workflow status¶

Show the status of the workflow.

-h, --help¶: show this help message and exit

--depth <depth>¶: querying depth

tm_client workflow submit¶

Submit the workflow using a previously uploaded description.

-h, --help¶: show this help message and exit

tm_client workflow upload¶

Upload a workflow description, updating any potentially existing description.

-h, --help¶: show this help message and exit

--file <filename>¶: path to YAML file from which workflow description should be read

tmclient.log module¶

class tmclient.log.InfoFilter(name='')¶

Bases: logging.Filter

Initialize a filter.

Initialize with the name of the logger which, together with its children, will have its events allowed through the filter. If no name is specified, allow every event.

filter(rec)¶

tmclient.log.LEVELS_TO_VERBOSITY = {0: 0, 10: 3, 20: 2, 30: 1}¶: Dict[int, int]: Mapping of logging level to verbosity

tmclient.log.VERBOSITY_TO_LEVELS = {0: 0, 1: 30, 2: 20, 3: 10}¶: Dict[int, int]: Mapping for logging verbosity to level

class tmclient.log.Whitelist(*whitelist)¶

Bases: logging.Filter

filter(record)¶

tmclient.log.configure_logging()¶

Configures the root logger for command line applications.

Two stream handlers will be added to the logger:

“out” that will direct INFO & DEBUG messages to the standard output

stream * “err” that will direct WARN, WARNING, ERROR, & CRITICAL messages to the standard error stream

tmclient.log.map_logging_verbosity(verbosity)¶

Parameters:

verbosity: int

logging verbosity level (0-4)

Returns:

A logging level as exported by logging module.

By default returns logging.NOTSET

Raises:

TypeError

when verbosity doesn’t have type int

ValueError

when verbosity is negative

tmclient package¶

Submodules¶

tmclient.base module¶

tmclient.api module¶

tm_client¶

tm_client acquisition¶

tm_client acquisition create¶

tm_client acquisition ls¶

tm_client acquisition rename¶

tm_client acquisition rm¶

tm_client channel¶

tm_client channel ls¶

tm_client channel rename¶

tm_client channel-image¶

tm_client channel-image download¶

tm_client experiment¶

tm_client experiment create¶

tm_client experiment ls¶

tm_client experiment rename¶

tm_client experiment rm¶

tm_client feature¶

tm_client feature ls¶

tm_client feature rename¶

tm_client feature rm¶

tm_client feature-values¶

tm_client feature-values download¶

tm_client jtproject¶

tm_client jtproject download¶

tm_client jtproject upload¶

tm_client microscope-file¶

tm_client microscope-file ls¶

tm_client microscope-file upload¶

tm_client object-type¶

tm_client object-type create¶

tm_client object-type ls¶

tm_client object-type rename¶

tm_client object-type rm¶

tm_client plate¶

tm_client plate create¶

tm_client plate ls¶

tm_client plate rename¶

tm_client plate rm¶

tm_client segmentation¶

tm_client segmentation download¶

tm_client segmentation upload¶

tm_client site¶

tm_client site ls¶

tm_client tools¶

tm_client tools log¶

tm_client tools ls¶

tm_client tools status¶

tm_client well¶

tm_client well ls¶

tm_client workflow¶

tm_client workflow download¶

tm_client workflow kill¶

tm_client workflow log¶

tm_client workflow resubmit¶

tm_client workflow status¶

tm_client workflow submit¶

tm_client workflow upload¶

tmclient.log module¶

tmclient.version module¶

Module contents¶