MorphoNet.Net Documentation

Docstring for the net.py module.

This API is used to directly interact with your data on MorphoNet

For any information for the installation go on https://pypi.org/project/morphonet/

class morphonet.net.Net(login='', passwd='', new_url=None, new_port=-1, token=None, id_user=-1)

Bases: object

Connect to the MorphoNet server.

Use your credentials to connect to MorphoNet

Parameters:

login (string) – your login in MorphoNet
passwd (string) – your password in MorphoNet
new_url (string, optional) – for developmental purpose, you can specify a new server that will be used to compute API request and get/upload MorphoNet data.
new_port (int, optional) – for developmental purpose, you can specify an other port

Returns:

return an object of morphonet which will allow you to upload or download data

Return type:

MorphoConnection

Examples

>>> import morphonet
>>> mn=morphonet.Net("yourlogin","yourpassword")

change_dataset_owner(new_owner_id)

Update the dataset on the server

Parameters:: new_owner_id (int) – Identifiant of the new owner

change_property_owner(id_property, new_owner_id)

Update the property on the server

Parameters:

id_property (int) – property to transfer
new_owner_id (int) – Identifiant of the new owner

clear_dataset()

Remove the 3D data and all properties for the selected dataset

Examples

>>> mn.clear_dataset()

clear_mesh_at(t, quality=-1, channel=-1)

Remove the 3D data for the selected dataset at a specified time point, for a quality and channel

Parameters:

t (int) – The time point to clear 3D data from
quality (int) – The quality of the 3D data
channel (int) – Wich channel of the object

Examples

>>> mn.clear_mesh_at(1,0,0)

create_dataset(name, minTime=0, maxTime=0, id_NCBI=0, id_type=0, spf=-1, dt=-1, serveradress=None)

To create a data in the MorphoNet database

Parameters:

name (string) – the given name of the dataset
minTime (int, optional) – the time first time point for 3D (or 2D) + t dataset, default: 0
maxTime (int, optional) – the last first time point for 3D (or 2D) + t dataset, default: 0
id_NCBI (int, optional) – the NCBI id attribute to the dataset
id_type (int, optional) –
the tType of dataset :
- 0 : Observed
- 1 : Simulated
- 2 : Drawed
spf (int , optional) – the second post fertilization for the first time point
dt (int , optional) – the delta time in seconds between two consecutive time points
serveradress (string , optional) – you own server adress

Examples

>>> mn.create_dataset("test set",minTime=1,maxTime=150)

delete_dataset()

Remove the selected dataset from the server

Examples

>>> mn.delete_dataset()

delete_dataset_by_id(id_dataset)

Remove the selected dataset from the server using its id

Examples

>>> mn.delete_dataset()

delete_image_at(t, channel=0)

Remove the raw image of the 3D dataset on the server, but only for a specific time point and channel

Parameters:

t (int) – The time point to delete raw images
channel (int, optional) – Which channel of the dataset
mn.delete_image_at(0) (>>>) –

delete_images(): Remove all the raw images from the server for the specified dataset

delete_primitive(name)

Delete a specific primitive (specified by its name) for the selected dataset

Parameters:: name (string) – Name of the primitive

Examples

>>> mn.delete_primitive("primitive to delete")

delete_primitives(): Clear all primitives existing for the selected dataset

delete_property_by_id(id_property)

Delete an property specified by its id on the server

Parameters:: id_property (string) – id of the property

Examples

>>> mn.delete_property_by_id("1")

delete_property_by_name(name)

Delete an property specified by its name on the server

Parameters:: name (string) – Name of the property

Examples

>>> mn.delete_property_by_name("property name")

get_annotation_by_id(id_property)

Retrieve the annotations for a property from MorphoNet

Parameters:: id_property (int) – ID of the property
Returns:: file – The annotation txt file for this property
Return type:: string

Examples

>>> data = mn.get_annotation_by_id(1)

get_cells_by_gene(gene_id): Retrieve the list of cells (with their expression value) for the gene passed in argument (gene id is the id inside the database) return a dictionnary with database id as key as value tuple containing (cell,stage,value)

get_cells_by_gene_by_stage(gene_id, stage_id): Retrieve the list of cells (with their expression value) for the gene and the stage passed in argument (gene id and stage id are the id inside the database) return a dictionnary with database id as key as value tuple containing (cell,value)

get_developmental_table(): Retrieve the corresponding developmental table of the specie of the dataset (avaible only for Ascidian ) return the list of developmentale table property (id,id_datasettype,period,stage,developmentaltstage,description,hpf)

get_genes(): Retrieve the list of genes for this specie return a list with (id,Gene Model, Gene Name, Unique Gene id)

get_genes_by_cell(cell_name): Retrieve the list of genes (with their expression value) for the cell name in argument return a dictionnary with database id as key as value tuple containing (stage,gene,value)

get_genes_by_cell_by_stage(cell_name, stage_id): Retrieve the list of genes (with their expression value) for the cell name and stage id in argument return a dictionnary with database id as key as value tuple containing (gene,value)

get_genes_by_stage(stage_id): Retrieve the list of genes (with their expression value) for the stage id in argument return a dictionnary with database id as key as value tuple containing (gene,cell,value)

get_group_by_name(name)

Return the group corresponding to a specific name

Parameters:: name (string) – the name of the group
Returns:: the id corresponding to the group, -1 if the group does not exist
Return type:: id_group

Examples

>>> mn.get_group_by_name("The ascidians")

get_guy_by_id(id_guy)

Return the person corresponding to an id

Parameters:: id_guy (int) – the id of the person you are looking for
Returns:: name , surname and login
Return type:: object

Examples

>>> mn.get_guy_by_id(1)

get_guy_by_name(name)

Return the person corresponding to a specific name and surname

Parameters:: name (string) – the name and surname separated by a space
Returns:: the id corresponding to the person, -1 if the person does not exist
Return type:: id_guy

Examples

>>> mn.get_guy_by_name("Faure Emmanuel")

get_image_at(t, channel=0)

Return the raw images (as a Numpy Matrix in uint8) from the server for the specified dataset :param t: The time point to upload raw images :type t: int :param channel: For which channel of the dataset :type channel: int, optional

Returns:: mat – the numpy matrix of the rawimage in uint8
Return type:: numpy

Examples

>>> mat=mn.get_image(1)

get_image_size(id_rawimage)

Get the dimensions as JSON in format ‘(x,y,z)’ of rawimage with given id

Parameters:: id (int) – ID of the RawImage (the same as the file name).
Returns:: dims – The dimensions as JSON in format ‘(x,y,z)’ of the rawimage. None if ID does not exist or there is an error
Return type:: string

get_mesh_at(t, quality=0, channel=0)

Retrieve the mesh on the server for the specified time, quality and channel

Parameters:

t (int) – The time point to get 3D data from
quality (int, optional) – Which quality of the dataset
channel (int, optional) – Which channel of the dataset

Returns:

obj – The 3D data for the mesh

Return type:

string

Examples

>>> data = mn.get_mesh_at(1)

get_number_of_mesh_at(t, quality=-1, channel=-1)

Get the number of 3D data mesh for the selected dataset at a specifid time point, for a quality and a channel

Parameters:

t (int) – The time point to get the number of 3D data from
quality (int) – The quality of the 3D data
channel (int) – Wich channel of the object

Returns:

count – the number of the 3D meshes for the specified configuration

Return type:

int

Examples

>>> mn.get_number_of_mesh_at(1,0,0)

get_objects_from_property_by_id(id_property)

Get the list of object of an property specified by its id

Parameters:: id_property (int) – ID of the property
Returns:: objects – List of key/value corresponding to a split to the property data
Return type:: list

Examples

>>> objetcs = mn.get_objects_from_property_by_id(1)

get_objects_from_property_by_name(name)

Get the list of object of an property specified by its name

Parameters:: name (string) – name of the property
Returns:: objects – List of key/value corresponding to a split to the property data
Return type:: list

Examples

>>> objetcs = mn.get_objects_from_property_by_name("property name")

get_properties()

List all properties for the selected dataset

Returns:: data – The list of properties
Return type:: list

get_property_annotated_by_id(id_property)

Retrieve directly the property annotated from MorphoNet

Parameters:: id_property (int) – ID of the property
Returns:: file – The property with the last annotation as a txt file in the MorphoNet Format
Return type:: string

Examples

>>> data = mn.get_property_annotated_by_id(1)

get_property_by_id(id_property)

Get the data of the property specified by its id

Parameters:: id_property (int) – ID of the property
Returns:: propertys – The data stored on the server
Return type:: bytes

Examples

>>> mn.get_property_by_id("property name")

get_property_by_name(name)

Get the data of the property specified by its name

Parameters:: name (string) – Name of the property
Returns:: property – The data stored on the server
Return type:: bytes

Examples

>>> mn.get_property_by_name("property name")

get_stages(): Retrieve the list of stages for this specie FROM “anissed all stages” return a dictionnary with stage database id as key and (Stage) as value

is_image_at(t, channel=0)

Test is the raw images from the server for the specified dataset :param t: The time point to upload raw images :type t: int :param channel: For which channel of the dataset :type channel: int, optional

Returns:: is – True if the raw image exist on the server
Return type:: bool

Examples

>>> mn.is_image_at(1)

list_dataset()

To display dataset you can access (even if you re not owner)

Examples

>>> mn.list_dataset()

It will display all your datasets like this >>> (id_set) set_name is data_type created by set_owner the creation_date

list_my_dataset()

To display the datasets you own

Examples

>>> mn.list_my_dataset()

Notes

It will display all your datasets like this >>> (id_set) set_name is data_type created by set_owner the creation_date

read_mesh(filename)

Read the mesh inside the given filename

Parameters:: filename (string) – the mesh file name
Returns:: obj – the mesh
Return type:: string

Examples

>>> mn.read_mesh("path/to/myfile.obj")

select_dataset_by_id(ids)

Select a dataset using an id

Parameters:: ids (int) – The dataset id to select

Examples

>>> mn.select_dataset_by_id(1)

select_dataset_by_name(name)

Select a dataset using is name

Parameters:: name (string) – The dataset name to select

Examples

>>> mn.select_dataset_by_name("The name")

share_dataset_with_group(id_group, role)

To share the current dataset with a specific group

Parameters:

id_group (int) – the id of the group
role (int) – the role (Manager : 1, Reader : 0 ) which will be attribute to the group

Examples

>>> mn.share_dataset_with_group(1,0)

share_dataset_with_user(id_user, role)

To share the current dataset with a specific user

Parameters:

id_user (int) – the id of the user
role (int) – the role (Manager : 1, Reader : 0 ) which will be attribute to the user

Examples

>>> mn.share_dataset_with_user(1,0)

share_property_by_id(id_property)

The property specified by its id become accessible to everyone you shared it (or public if you shared the property with public)

Parameters:: id_property (int) – ID of the property

Examples

>>> objetcs = mn.share_property_by_id(1)

show_properties_type(): Display all properties type storing fomats

unshare_dataset_with_group(id_group)

To unshare the current dataset with a specific group

Parameters:: id_group (int) – the id of the group

Examples

>>> mn.unshare_dataset_with_group(1)

unshare_dataset_with_user(id_user)

To unshare the current dataset with a specific user

Parameters:: id_user (int) – the id of the user

Examples

>>> mn.unshare_dataset_with_user(1)

unshare_property_by_id(id_property)

The property specified by its id become unaccessible to everyone you shared it (or public if you shared the property with public)

Parameters:

id_property (int) –
property (ID of the) –

Examples

>>> objetcs = mn.unshare_property_by_id(1)

update_dataset(dataset_name='', minTime=-1, maxTime=-1, id_NCBI=-1, id_type=-1)

Change specified values for the selected dataset

Parameters:

dataset_name (string, optional) – New name of the dataset
minTime (int, optional) – New minimal time point
maxTime (int, optional) – New maximum time point
id_NCBI (int, optional) – New taxonomy category id
id_type (int, optional) – New dataset stored type

Examples

>>> mn.update_dataset("Changing name only")

or

>>> mn.update_dataset("new name",1,1,1000,1)

update_rawimage_link(id_rawimage, link)

Updates the link of a Rawimage with given id

Parameters:

id (int) – ID of the RawImage (the same as the file name).
link (string) – new link to replace the previous one with

upload_description(description)

Change description of the selected dataset on the server

Parameters:: description (string) – New description to upload

Examples

>>> mn.upload_description("The new description attached")

upload_image_at(t, rawdata, voxel_size='1,1,1', channel=0, scale=1)

Upload the dataset raw images with a scale value for a specified time, channel, It will erase any previous uploaded rawimages at this time point :param t: The time point to upload raw images :type t: int :param rawdata: The numpy array of the raw images of the dataset :type rawdata: uint8 :param channel: For which channel of the dataset :type channel: int, optional :param scale: Scale the raw images during the display to match the 3D data :type scale: float, optional

Returns:: id – The id of the raw image created on the server
Return type:: int

Examples

>>> im = imread(filepath) #Read your image
>>> factor=2 #specify the rescale Factor
>>> im=np.uint8(255*np.float32(im[::factor,::factor,::factor])/im.max())  #Convert it in 8 bits
>>> mn.upload_image_at(1,im,scale=factor)

upload_mesh_at(t, obj, quality=0, channel=0, link='null', texture=None, material=None, ttype='bmp', center=None)

Upload a new mesh (3D data) to a specific time point, for a quality and channel given. You can upload a texture by giving a texture and a material, specifying the texture format In order to add mutliple meshes at the same time point, you can call mutliple times the upload_mesh function :param t: The time point to set 3D data :type t: int :param obj: The content of the 3D data :type obj: bytes :param quality: Which quality of the dataset :type quality: int, optional :param channel: Which channel of the dataset :type channel: int, optional :param link: Do not specify this one if you don’t know what you are doing !! If bundle already exist for this mesh on the server, specify it :type link: string, optional :param texture: The texture data content that will be applied to the mesh :type texture: bytes, optional :param material: If texture is set, the name of the material that will be applied after applying the texure :type material: string, optional :param ttype: If texture is set, the file format for the texture

Returns:: id – The id of the mesh created on the server
Return type:: int

Examples

>>> #Specify a file on the hard drive by path, with rights
>>> f = open(filepath,"r+")
>>> #load content of file inside variable
>>> content = f.read()
>>> mn.upload_mesh_at(1,content,0,0)
>>> f.close()

upload_mesh_with_primitive_at(t, obj, quality=0, channel=0)

Upload a new mesh (3D data) to a specific time point, for a quality and channel given but using a primitive object

Parameters:

t (int) – The time point to store 3D data
obj (string) – The mesh of the 3D data
quality (int, optional) – Which quality of the dataset
channel (int, optional) – Which channel of the dataset

Returns:

id – The id of the mesh created on the server

Return type:

int

Examples

>>>
>>> with open('mymesh.obj','r') as f: #Specify a file on the hard drive by path, with rights
>>>     obj = f.read()   #load mesh of the file inside variable
>>> mn.upload_mesh_with_primitive_at(1,obj)

upload_primitive(name, obj)

Create a reusable 3D format instance in the database

Parameters:

name (string) – Name of the primitive
obj (bytes) – The content of the primitive (3D Data)

Returns:

id – The id of the primitive created on the server

Return type:

int

Examples

>>> with open('myprimitive.obj','r') as f: #Specify a file on the hard drive by path, with rights
>>>     obj = f.read()   #load mesh of the file inside variable
>>> mn.upload_primitive("a new primitive",obj)

upload_property(name, field)

Create a new property in the database

Parameters:

name (string) – Name of the property
field (bytes) – The content of the property (text Data respecting the corresponding format)

Returns:

id (int) – The id of the property created on the server
Examples_get_objects
——–
>>> #Specify a file on the hard drive by path, with rights
>>> file = open(filepath,”r+”)
>>> #load content of file inside variable
>>> content = f.read()
>>> mn.upload_property(“a new property”,content)