Merge pull request #48 from qbicsoftware/release/1.4.0

Release/1.4.0

drop-boxes/register-omero-metadata/backendinterface.py

@@ -0,0 +1,381 @@
+
+"""Interface to the image management server
+This module contains the functionality to upload and download
+imaging data (raw and metadata) form the OMERO server (v5.4).
+It requires that the following software be installed within the Python
+environment you are loading this module:
+	* OMERO.cli (https://docs.openmicroscopy.org/omero/5.4.0/users/cli/index.html)
+	* OMERO Python language bindings (https://docs.openmicroscopy.org/omero/5.4.0/developers/Python.html)
+This code is based on the following documentation:
+    https://docs.openmicroscopy.org/omero/5.4.0/developers/Python.html
+It contains the following functions:
+    * omero_connect - connects to server
+    * TODO...
+    
+"""
+
+
+def omero_connect(usr, pwd, host, port):
+    """
+    Connects to the OMERO Server with the provided username and password.
+
+    Args:
+        usr: The username to log into OMERO
+        pwd: a password associated with the given username
+        host: the OMERO hostname
+        port: the port at which the OMERO server can be reached
+
+    Returns:
+        Connected BlitzGateway to the OMERO Server with the provided credentials
+
+    """
+    from omero.gateway import BlitzGateway
+
+    conn = BlitzGateway(usr, pwd, host=host, port=port)
+    connected = conn.connect()
+    conn.setSecure(True)
+
+    if not connected:
+        print("Error: Connection not available")
+
+    return conn
+
+def print_data_ids(conn):
+    """
+        Prints all IDs of the data objects(Projects, Datasets, Images) associated with the logged in user on the OMERO server
+
+        Args:
+            conn: Established Connection to the OMERO Server via a BlitzGateway
+
+        Returns:
+            Nothing except a printed text output to console
+
+        """
+
+    for project in conn.getObjects("Project"):
+        print('project: ' + str(project.getName()) + ' -- ' + str(project.getId()))
+
+        for dataset in project.listChildren():
+            print('ds: ' + str(dataset.getName()) + ' -- ' + str(dataset.getId()))
+
+            for image in dataset.listChildren():
+                print('img: ' + str(image.getName()) + ' -- ' + str(image.getId()))
+
+def get_omero_dataset_id(conn, openbis_project_id, openbis_sample_id):
+    """
+           Prints all IDs of the data objects(Projects, Datasets, Images) associated with the logged in user on the OMERO server
+
+           Args:
+               conn: Established Connection to the OMERO Server via a BlitzGateway
+               openbis_project_id: Id specifying the project information stored on OpenBIS
+               openbis_sample_id: Id specifying the sample information stored on OpenBIS
+           Returns:
+               omero_dataset_id:  Id specifying the dataset information stored on OMERO
+
+           """
+    omero_dataset_id = -1
+    found_id = False
+
+    my_exp_id = conn.getUser().getId()
+    default_group_id = conn.getEventContext().groupId
+
+    for project in conn.getObjects("Project"):
+
+        if found_id:
+            break
+
+        if project.getName() == openbis_project_id:
+            for dataset in project.listChildren():
+
+                if dataset.getName() == openbis_sample_id:
+                    omero_dataset_id = dataset.getId()
+
+                    found_id = True
+                    break
+
+    return omero_dataset_id
+
+def register_image_file(file_path, project_id, sample_id, usr, pwd, host, port=4064):
+    """
+    This function imports an image file to an omero server using the OMERO.cli (using Bio-formats)
+    This function assumes the OMERO.cli is installed
+    Example:
+        register_image_file("data/test_img.nd2", "project_x", "sample_y",
+         "joe_usr", "joe_pwd", "192.168.2.2")
+    Args:
+        file_path (string): the path to the fastq file to validate
+        project_id (string): the corresponding project ID in openBIS server
+        sample_id (string): the corresponding sample ID in openBIS server
+        usr (string): username for the OMERO server
+        pwd (string): password for the OMERO server
+        host (string): OMERO server address
+        port (int): OMERO server port
+    Returns:
+        list of strings: list of newly generated omero IDs for registered images
+                (a file can contain many images)
+    """
+
+    import subprocess
+
+    image_ids = []
+
+    conn = omero_connect(usr, pwd, host, str(port))
+    ds_id = get_omero_dataset_id(conn, project_id, sample_id)
+
+    if ds_id != -1:
+
+        cmd = "omero-importer -s " + host + " -p " + str(port) + " -u " + usr + " -w " + pwd + " -d " + str(int(ds_id)) + " " + file_path
+        print("----cmd: " + cmd)
+
+        proc = subprocess.Popen(cmd,
+                            stdout=subprocess.PIPE,
+                            stderr=subprocess.PIPE,
+                            shell=True,
+                            universal_newlines=True)
+
+        std_out, std_err = proc.communicate()
+
+        print("std_out: " + std_out)
+        print("std_err: " + std_err)
+        print("return_code: " + str(proc.returncode))
+
+        if int(proc.returncode) == 0:
+
+            print("-->" + std_out)
+
+            fist_line = std_out.splitlines()[0]
+            image_ids = fist_line[6:].split(',')
+
+            print("id list: " + str(image_ids))
+
+        else:
+            print("return code fail")
+
+    else:
+        print("invalid sample_id")
+
+    return image_ids
+
+def register_image_file_with_dataset_id(file_path, dataset_id, usr, pwd, host, port=4064):
+    """
+    This function imports an image file to an omero server using the OMERO.cli (using Bio-formats)
+    This function assumes the OMERO.cli is installed
+    Example:
+        register_image_file("data/test_img.nd2", 10,
+         "joe_usr", "joe_pwd", "192.168.2.2")
+    Args:
+        file_path (string): the path to the fastq file to validate
+        dataset_id (string): the ID of the omero dataset
+        usr (string): username for the OMERO server
+        pwd (string): password for the OMERO server
+        host (string): OMERO server address
+        port (int): OMERO server port
+    Returns:
+        list of strings: list of newly generated omero IDs for registered images
+                (a file can contain many images)
+    """
+
+    import subprocess
+
+    image_ids = []
+
+    ds_id = dataset_id
+
+    if ds_id != -1:
+
+        cmd = "omero-importer -s " + host + " -p " + str(port) + " -u " + usr + " -w " + pwd + " -d " + str(int(ds_id)) + " " + file_path
+
+        proc = subprocess.Popen(cmd,
+                            stdout=subprocess.PIPE,
+                            stderr=subprocess.PIPE,
+                            shell=True,
+                            universal_newlines=True)
+
+        std_out, std_err = proc.communicate()
+
+        if int(proc.returncode) == 0:
+
+            fist_line = std_out.splitlines()[0]
+            image_ids = fist_line[6:].split(',')
+
+        else:
+            image_ids = -1
+
+    else:
+        image_ids = -1
+
+    return image_ids
+
+
+########################################
+#functions to register numpy arrays
+
+def generate_array_plane(new_img):
+    """
+    TODO
+    """
+
+    img_shape = new_img.shape
+    size_z = img_shape[4]
+    size_t = img_shape[0]
+    size_c = img_shape[1]
+
+    for z in range(size_z):              # all Z sections
+        for c in range(size_c):          # all channels
+            for t in range(size_t):      # all time-points
+
+                new_plane = new_img[t, c, :, :, z]
+                yield new_plane
+
+def create_array(conn, img, img_name, img_desc, ds):
+    """
+    TODO
+    """
+
+    dims = img.shape
+    z = dims[4]
+    t = dims[0]
+    c = dims[1]
+
+    new_img = conn.createImageFromNumpySeq(generate_array_plane(img),
+                                           img_name,
+                                           z, c, t,
+                                           description=img_desc,
+                                           dataset=ds)
+
+    return new_img.getId()
+
+def register_image_array(img, img_name, img_desc, project_id, sample_id, usr, pwd, host, port=4064):
+    """
+    This function imports a 5D (time-points, channels, x, y, z) numpy array of an image
+    to an omero server using the OMERO Python bindings 
+    Example:
+        register_image_array(hypercube, "tomo_0", "this is a tomogram",
+         "project_x", "sample_y", "joe_usr", "joe_pwd", "192.168.2.2")
+    Args:
+        file_path (string): the path to the fastq file to validate
+        project_id (string): the corresponding project ID in openBIS server
+        sample_id (string): the corresponding sample ID in openBIS server
+        usr (string): username for the OMERO server
+        pwd (string): password for the OMERO server
+        host (string): OMERO server address
+        port (int): OMERO server port
+    Returns:
+        int: newly generated omero ID for registered image array
+    """
+
+    img_id = -1
+    save_flag = 0
+
+    conn = omero_connect(usr, pwd, host, str(port))
+
+    for project in conn.getObjects("Project"):
+        if project.getName() == project_id:
+            for dataset in project.listChildren():
+                if dataset.getName() == sample_id:
+
+                    img_id = create_array(conn, img, img_name, img_desc, dataset)
+
+                    save_flag = 1
+                    break
+        if save_flag == 1:
+            break
+
+    return int(img_id)
+
+def get_image_array(conn, image_id):
+    """
+    This function retrieves an image from an OMERO server as a numpy array
+    TODO
+    """
+
+    import numpy as np
+
+    image = conn.getObject("Image", image_id)
+
+    #construct numpy array (t, c, x, y, z)
+
+    size_x = image.getSizeX()
+    size_y = image.getSizeY()
+    size_z = image.getSizeZ()
+    size_c = image.getSizeC()
+    size_t = image.getSizeT()
+
+    # X and Y fields have to be aligned this way since during generation of the image from the numpy array the 2darray is expected to be (Y,X)
+    # See Documentation here https://downloads.openmicroscopy.org/omero/5.5.1/api/python/omero/omero.gateway.html#omero.gateway._BlitzGateway
+    hypercube = np.zeros((size_t, size_c, size_y, size_x, size_z))
+
+    pixels = image.getPrimaryPixels()
+
+    for t in range(size_t):
+        for c in range(size_c):
+            for z in range(size_z):
+                plane = pixels.getPlane(z, c, t)      # get a numpy array.
+                hypercube[t, c, :, :, z] = plane
+
+    return hypercube
+
+################################
+
+def add_annotations_to_image(conn, image_id, key_value_data):
+    """
+    TODO
+    """
+
+    import omero
+
+    map_ann = omero.gateway.MapAnnotationWrapper(conn)
+    # Use 'client' namespace to allow editing in Insight & web
+    namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
+    map_ann.setNs(namespace)
+    map_ann.setValue(key_value_data)
+    map_ann.save()
+
+    image = conn.getObject("Image", image_id)
+    # NB: only link a client map annotation to a single object
+    image.linkAnnotation(map_ann)
+
+    return 0
+
+
+#########################
+##app
+
+from optparse import OptionParser
+
+###OMERO server info
+USERNAME = "usr"
+PASSWORD = "pwd"
+HOST = "host"
+PORT = 4064
+
+
+def get_args():
+    parser = OptionParser()
+    parser.add_option('-f', '--file', dest='file_path', default="None", help='file to register')
+    parser.add_option('-d', '--dataset', dest='dataset_id', default="None", help='dataset id for registration')
+
+    parser.add_option('-p', '--project', dest='project_id', default="None", help='project id for dataset id retrieval')
+    parser.add_option('-s', '--sample', dest='sample_id', default="None", help='sample id for dataset id retrieval')
+
+    (options, args) = parser.parse_args()
+    return options
+
+if __name__ == '__main__':
+
+    args = get_args()
+
+    if args.file_path != "None":
+        img_ids = register_image_file_with_dataset_id(args.file_path, int(args.dataset_id), USERNAME, PASSWORD, HOST)
+
+        id_str = ""
+        for id_i in img_ids:
+            id_str = id_str + id_i + " "
+
+        print id_str
+    else:
+
+        conn = omero_connect(USERNAME, PASSWORD, HOST, str(PORT))
+        ds_id = get_omero_dataset_id(conn, str(args.project_id), str(args.sample_id))
+
+        print ds_id