Source code for tissuumaps.jupyter

Module used to run TissUUmaps from a Jupyter Notebook or from Jupyter Lab.

import json
import logging
import os
import threading
import time
import uuid
import warnings
from pathlib import Path

import click
from IPython.core.display import display
from IPython.display import HTML, Javascript

from tissuumaps import views

def secho(text, file=None, nl=None, err=None, color=None, **styles):

def echo(text, file=None, nl=None, err=None, color=None, **styles):

click.echo = echo
click.secho = secho

[docs]def opentmap(path, port=5100, host="localhost", height=700): """ Open a tmap project Args: path (str): The path to a tmap file port (int): The port to run the TissUUmaps server host (str): The host to run the TissUUmaps server height (int): The height of the jupyter iframe Returns: TissUUmapsViewer: The TissUUmaps viewer """ path = os.path.abspath(path) parts = Path(path).parts server = TissUUmapsServer(slideDir=parts[0], port=port, host=host) return server.viewer(parts[-1] + "?path=" + os.path.join(*parts[1:-1]), height)
[docs]def loaddata( images=[], csvFiles=[], xSelector="x", ySelector="y", keySelector=None, nameSelector=None, colorSelector=None, piechartSelector=None, shapeSelector=None, scaleSelector=None, fixedShape=None, scaleFactor=1, colormap=None, compositeMode="source-over", boundingBox=None, port=5100, host="localhost", height=700, tmapFilename="_project", plugins=[], ): """ Load data in TissUUmaps Args: images (list | str): List of images or single image to display csvFiles (list | str): List of csv files or single csv file to display xSelector (str): Name of the csv column defining the X coordinates ySelector (str): Name of the csv column defining the Y coordinates keySelector (str): Name of the csv column defining the grouping key nameSelector (str): Name of the csv column defining the group name colorSelector (str): Name of the csv column defining the group color piechartSelector (str): Name of the csv column defining pie-charts shapeSelector (str): Name of the csv column defining markers' shape scaleSelector (str): Name of the csv column defining markers' scale fixedShape (int): Name of the markers' shape scaleFactor (int): Global scale of markers colormap (str): Name of the colormap used if colorSelector is set compositeMode: (str): Composite mode used for images boundingBox (list): [X,Y,W,H] of the bounding box to display port (int): The port to run the TissUUmaps server host (str): The host to run the TissUUmaps server height (int): The height of the jupyter iframe tmapFilename (str): Name of the project file that will be created plugins (list): List of plugins to add to the tmap project Returns: TissUUmapsViewer: The TissUUmaps viewer """ # make str input to arrays: if isinstance(images, str): images = [images] if isinstance(csvFiles, str): csvFiles = [csvFiles] # make all paths absolute: images = [os.path.abspath(f) for f in images] csvFiles = [os.path.abspath(f) for f in csvFiles] # make all paths relative to project file: rootPath = os.path.commonpath( [os.path.dirname(f) for f in images] + [os.path.dirname(f) for f in csvFiles] ) images = [os.path.relpath(f, rootPath) for f in images] csvFiles = [os.path.relpath(f, rootPath) for f in csvFiles] # Create json TMAP file: jsonTmap = { "compositeMode": compositeMode, "filename": "", "layers": [ {"name": os.path.basename(layer), "tileSource": layer + ".dzi"} for layer in images ], "hideTabs": True, "markerFiles": [], "plugins": plugins, } if boundingBox: jsonTmap["boundingBox"] = { "x": boundingBox[0], "y": boundingBox[1], "width": boundingBox[2], "height": boundingBox[3], } if csvFiles: expectedHeader = { "X": xSelector, "Y": ySelector, "gb_col": keySelector, "gb_name": nameSelector, "cb_cmap": colormap, "cb_col": colorSelector, "scale_col": scaleSelector, "scale_factor": scaleFactor, "pie_col": piechartSelector, "shape_col": shapeSelector, "shape_fixed": fixedShape, "cb_gr_dict": "", "shape_gr_dict": "", "opacity": 1, } expectedRadios = { "cb_col": colorSelector is not None, "cb_gr": colorSelector is None, "cb_gr_rand": False, "cb_gr_dict": False, "cb_gr_key": True, "pie_check": piechartSelector is not None, "scale_check": scaleSelector is not None, "shape_gr": shapeSelector is None and fixedShape is None, "shape_gr_rand": shapeSelector is None and fixedShape is None, "shape_gr_dict": False, "shape_col": shapeSelector is not None, "shape_fixed": fixedShape is not None, } if len(csvFiles) == 1: csvFiles = csvFiles[0] jsonTmap["markerFiles"] = [ { "comment": "All markers", "path": csvFiles, "title": "Download markers", "autoLoad": True, "hideSettings": True, "expectedHeader": expectedHeader, "expectedRadios": expectedRadios, "uid": "markers", } ] tmapFile = os.path.join(rootPath, f"{tmapFilename}.tmap") print("Creating project file", tmapFile) with open(tmapFile, "w") as f: json.dump(jsonTmap, f) return opentmap(os.path.abspath(tmapFile), port=port, host=host, height=height)
[docs]class TissUUmapsViewer: """ Class representing a TissUUmaps viewer instance """ def __init__(self, server, image, height=700): self.server = server self.image = image = "tissUUmapsViewer_" + str(uuid.uuid1()).replace("-", "")[0:10] iframe = ( '<iframe src="{src}" style="width: {width}; ' 'height: {height}; border: none" id="{id}" allowfullscreen></iframe>' ) src = f"http://{}:{self.server.port}/{self.image}" print("Loading url: ", src) self.htmlIFrame = HTML( iframe.format(width="100%", height=str(height) + "px", src=src, ) display(self.htmlIFrame) time.sleep(2)
[docs] def screenshot(self): """ Capture the TissUUmaps viewport and display image in the Notebook. """ screenshot_id = + "_" + str(uuid.uuid1()).replace("-", "")[0:6] display( Javascript( """ function listenToMessages_""" + screenshot_id + """(evt){ if ( != "screenshot") return; window.removeEventListener("message", listenToMessages_""" + screenshot_id + """); try { IPython.notebook.kernel.execute( `from IPython.display import update_display, HTML` ) IPython.notebook.kernel.execute( `obj = HTML("<img src='``'/>")` ) IPython.notebook.kernel.execute( `update_display(obj, display_id="display_out_""" + screenshot_id + """" )`) } catch (e) { // vscode or jupyterLab can not communicate back... if (e instanceof ReferenceError) { document.getElementById("img_out_""" + screenshot_id + """").src =; let newNode = document.createElement("span"); newNode.innerHTML = "Warning: run viewer.screenshot in a \ classical Jupyter Notebook if you want the screenshot \ to be saved."; document.getElementById("img_out_""" + screenshot_id + """").parentElement.insertBefore( newNode, document.getElementById("img_out_""" + screenshot_id + """")); } } } var iframe = document.getElementById('""" + + """'); window.addEventListener("message", listenToMessages_""" + screenshot_id + """); iframe.contentWindow.postMessage({'module':'','function':'','arguments':'[]'},'*'); """ ) ) display( HTML("<img src='' id='img_out_" + screenshot_id + "'/>"), display_id="display_out_" + screenshot_id, )
[docs]class TissUUmapsServer: """ Class representing a TissUUmaps server instance """ def __init__(self, slideDir, port=5000, host=""): log = logging.getLogger("werkzeug") log.setLevel(logging.ERROR) log = logging.getLogger("pyvips") log.setLevel(logging.ERROR) warnings.filterwarnings("ignore") self.started = False self.port = port = host self.slideDir = slideDir["SLIDE_DIR"] = slideDir def startServer(): views.setup("", port=self.port, threaded=True, debug=False) if TissUUmapsServer.is_port_in_use(self.port): log.warning( f"Port {self.port} already in use. " "Impossible to start TissUUmaps server." ) return thread = threading.Thread(target=startServer) thread.setdaemon = False thread.start() self.started = True @staticmethod def is_port_in_use(port): import socket with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: return s.connect_ex(("localhost", port)) == 0 def viewer(self, image, height=700): viewer = TissUUmapsViewer(self, image, height) return viewer
if __name__ == "__main__": pass