Documentation and minor bug fixes [skip ci]

README.md

@@ -19,13 +19,13 @@ segmentation and standardized reporting", which has been published in [Frontiers
 Or
 * git clone --single-branch --branch master https://github.com/dbouget/Raidionics-Slicer.git /path/to/folder/.  
 
-2.3 Download and install Docker (see Section 3).  
+2.3 Download and install Docker (see below).  
 
 2.3 Load the plugin into 3DSlicer:   
 	∘ All Modules > Extension Wizard.  
 	∘ Developer Tools > Extension Wizard.  
 	∘ Select Extension > point to the folder (second Raidionics) and add it to the path (tick the small box at the bottom).  
-A restart of 3DSlicer is necessary after the initial launch with the plugin to have the proper Python environment.  
+:warning: A restart of 3DSlicer is necessary after the initial launch with the plugin to have the proper Python environment.  
 </details>
 
 <details open>

Raidionics/Raidionics/src/RaidionicsLogic.py

@@ -152,11 +152,6 @@ def thread_doit(self, model_parameters):
         try:
             self.main_queue_start()
             self.logic_target_space = "neuro_diagnosis" if modelTarget == "Neuro" else "mediastinum_diagnosis"
-            # if model_parameters.json_dict['task'] == 'Diagnosis':
-            #     if model_parameters.json_dict['organ'] == 'Brain':
-            #         SharedResources.getInstance().user_diagnosis_configuration['Default']['task'] = 'neuro_diagnosis'
-            #     elif model_parameters.json_dict['organ'] == 'Mediastinum':
-            #         SharedResources.getInstance().user_diagnosis_configuration['Default']['task'] = 'mediastinum_diagnosis'
 
             self.executeDocker(dockerName, modelName, dataPath, iodict, inputs, outputs, params, widgets)
             if not self.abort:
@@ -368,20 +363,21 @@ def executeDocker(self, dockerName, modelName, dataPath, iodict, inputs, outputs
                     if iodict[item]["type"] == "volume":
                         # print(inputs[item])
                         input_node_name = inputs[item].GetName()
-                        #try:
-                        img = sitk.ReadImage(sitkUtils.GetSlicerITKReadWriteAddress(input_node_name))
-                        input_sequence_type = iodict[item]["sequence_type"]
-                        fileName = 'input_' + input_sequence_type + self.file_extension_docker
-                        # @TODO. hard-coding to improve.
-                        if input_sequence_type == "T1-CE":
-                            fileName = 'input_t1gd' + self.file_extension_docker
-                        inputDict[item] = fileName
-                        input_timestamp_order = iodict[item]["timestamp_order"]
-                        os.makedirs(str(os.path.join(SharedResources.getInstance().data_path, "T" + input_timestamp_order)))
-                        sitk.WriteImage(img, str(os.path.join(SharedResources.getInstance().data_path,
-                                                              "T" + input_timestamp_order, fileName)))
-                        #except Exception as e:
-                        #    print(e.message)
+                        try:
+                            img = sitk.ReadImage(sitkUtils.GetSlicerITKReadWriteAddress(input_node_name))
+                            input_sequence_type = iodict[item]["sequence_type"]
+                            fileName = 'input_' + input_sequence_type + self.file_extension_docker
+                            # @TODO. hard-coding to improve.
+                            if input_sequence_type == "T1-CE":
+                                fileName = 'input_t1gd' + self.file_extension_docker
+                            inputDict[item] = fileName
+                            input_timestamp_order = iodict[item]["timestamp_order"]
+                            os.makedirs(str(os.path.join(SharedResources.getInstance().data_path, "T" + input_timestamp_order)))
+                            sitk.WriteImage(img, str(os.path.join(SharedResources.getInstance().data_path,
+                                                                  "T" + input_timestamp_order, fileName)))
+                        except Exception as e:
+                            print("Issue preparing input volume.")
+                            print(traceback.format_exc())
                     elif iodict[item]["type"] == "configuration":
                         generate_backend_config(SharedResources.getInstance().data_path,
                                                 iodict, self.logic_target_space, modelName)

Raidionics/Raidionics/src/gui/Diagnosis/DiagnosisInterfaceWidget.py

@@ -154,10 +154,7 @@ def populate_local_diagnosis(self):
                 self.local_diagnosis_selector_combobox.addItem(name, idx + 1)
 
     def on_diagnosis_selection(self, index):
-        if index < 1 or self.local_diagnosis_selector_combobox.count == 1:
-            return
-
-        jsonIndex = self.local_diagnosis_selector_combobox.itemData(index)
+        selected_model = self.local_diagnosis_selector_combobox.currentText
         selected_diagnosis = self.local_diagnosis_selector_combobox.currentText
         if SharedResources.getInstance().global_active_model_update:
             dl_req = check_local_diagnosis_for_update(selected_diagnosis)
@@ -167,11 +164,11 @@ def on_diagnosis_selection(self, index):
                 diag.exec()
 
         self.diagnosis_model_parameters.destroy()
-        json_model = self.json_diagnoses[jsonIndex - 1]
+        json_model = self.find_json_model(selected_model_name=selected_model)
         self.diagnosis_model_parameters.create(json_model)
 
-        if "briefdescription" in self.json_diagnoses[jsonIndex - 1]:
-            tip = self.json_diagnoses[jsonIndex - 1]["briefdescription"]
+        if "briefdescription" in json_model:
+            tip = json_model["briefdescription"]
             tip = tip.rstrip()
             self.local_diagnosis_selector_combobox.setToolTip(tip)
         else:
@@ -189,7 +186,7 @@ def on_diagnosis_selection(self, index):
             if new_docker_status:
                 self.diagnosis_available_signal.emit(True)
             else:
-                tip = 'The required Docker image could not be downloaded, maybe because of read/write access rights or because the image is private:\n'
+                tip = 'The required Docker image could not be downloaded, because of inadequet access rights or missing Docker installation.\n'
                 tip += '   * Open the command line editor (On Windows, type \'cmd\' in the search bar.)\n'
                 tip += '   * Copy and execute: docker image pull {}\n'.format(self.model_parameters.dockerImageName)
                 tip += '   * Wait for the download to be complete, then exit the popup.\n'
@@ -239,3 +236,11 @@ def on_cloud_diagnosis_download_selected(self):
         # if True: #success:
         self.populate_local_diagnosis()
         self.populate_cloud_diagnosis()
+
+    def find_json_model(self, selected_model_name):
+        json_model = None
+        for m in self.jsonModels:
+            if m['name'] == selected_model_name:
+                json_model = m
+                break
+        return json_model

Raidionics/Raidionics/src/gui/RaidionicsWidget.py

@@ -129,6 +129,8 @@ def setup_user_interactions_widget(self):
         self.tasks_tabwidget.addTab(self.base_segmentation_widget, 'Segmentation')
         self.base_diagnosis_widget = BaseDiagnosisWidget(self.parent)
         self.tasks_tabwidget.addTab(self.base_diagnosis_widget, 'Reporting (RADS)')
+        self.base_diagnosis_widget.setEnabled(False)
+        self.base_diagnosis_widget.setToolTip("Currently disabled for maintenance, please use Raidionics in the meantime.")
         self.logging_textedit = qt.QTextEdit()
         #self.logging_textedit.setEnabled(False)
         self.logging_textedit.setReadOnly(True)

Raidionics/Raidionics/src/gui/Segmentation/ModelsInterfaceWidget.py

@@ -143,10 +143,10 @@ def populate_cloud_models(self):
             self.cloud_model_download_pushbutton.setEnabled(False)
 
     def on_model_selection(self, index):
-        # @TODO. Maybe need a flush method to remove old models, in case the users don't know how to do it themselves?
-        if index < 1 or self.local_model_selector_combobox.count == 1:
-            return
-
+        """
+        Updates the model parameters GUI part based on the currently selected model.
+        The index parameter is currently not used, as the current combobox text is directly retrieved and used.
+        """
         selected_model = self.local_model_selector_combobox.currentText
         # @TODO. Should also check if the files are still on disk, before sending the OK signal?
         # @TODO. Should also check for an update of the docker image by comparing sha numbers?
@@ -157,12 +157,14 @@ def on_model_selection(self, index):
                 diag.set_model_name(selected_model)
                 diag.exec()
         self.model_parameters.destroy()
-        jsonIndex = self.local_model_selector_combobox.itemData(index)
-        json_model = self.jsonModels[jsonIndex - 1]
+        json_model = self.find_json_model(selected_model_name=selected_model)
+        if not json_model:
+            return
+
         self.model_parameters.create(json_model)
 
-        if "briefdescription" in self.jsonModels[jsonIndex - 1]:
-            tip = self.jsonModels[jsonIndex - 1]["briefdescription"]
+        if "briefdescription" in json_model:
+            tip = json_model["briefdescription"]
             tip = tip.rstrip()
             self.local_model_selector_combobox.setToolTip(tip)
         else:
@@ -180,7 +182,7 @@ def on_model_selection(self, index):
             if new_docker_status:
                 self.segmentation_available_signal.emit(True)
             else:
-                tip = 'The required Docker image could not be downloaded, maybe because of read/write access rights or because the image is private:\n'
+                tip = 'The required Docker image could not be downloaded, because of inadequate access rights or missing Docker installation.\n'
                 tip += '   * Open the command line editor (On Windows, type \'cmd\' in the search bar.)\n'
                 tip += '   * Copy and execute: docker image pull {}\n'.format(self.model_parameters.dockerImageName)
                 tip += '   * Wait for the download to be complete, then exit the popup.\n'
@@ -276,3 +278,11 @@ def on_model_details_selected(self):
         popup.setWindowTitle('Exhaustive description for {}'.format(self.local_model_selector_combobox.currentText))
         popup.setText(tip)
         x = popup.exec_()
+
+    def find_json_model(self, selected_model_name):
+        json_model = None
+        for m in self.jsonModels:
+            if m['name'] == selected_model_name:
+                json_model = m
+                break
+        return json_model

Raidionics/Raidionics/src/utils/backend_utilities.py

@@ -6,7 +6,21 @@
 from src.utils.resources import SharedResources
 
 
-def generate_backend_config(input_folder, parameters, logic_target_space, model_name):
+def generate_backend_config(input_folder: str, parameters, logic_target_space: str, model_name: str) -> None:
+    """
+    Preparing the configuration file to be used as input by raidionics_rads_lib (processing backend).
+
+    Parameters
+    ----------
+    input_folder: str
+         Folder to be used as input by the backend.
+    parameters: ?
+        Not used anymore
+    logic_target_space: str
+        Description of the targeted medical specialty, between neuro and mediastinum for now.
+    model_name: str
+        Name of the model to be executed in the backend.
+    """
     try:
         rads_config = configparser.ConfigParser()
         rads_config.add_section('Default')
@@ -19,6 +33,7 @@ def generate_backend_config(input_folder, parameters, logic_target_space, model_
         rads_config.set('System', 'model_folder', '/home/ubuntu/resources/models')
         rads_config.set('System', 'pipeline_filename', '/home/ubuntu/resources/models/' + model_name + '/pipeline.json')
         rads_config.add_section('Runtime')
+        # @TODO. The backend disregards those parameters after the latest RADS lib update, has to be fixed
         rads_config.set('Runtime', 'reconstruction_method',
                         SharedResources.getInstance().user_configuration['Predictions']['reconstruction_method'])
         rads_config.set('Runtime', 'reconstruction_order',

Raidionics/Raidionics/src/utils/io_utilities.py

@@ -7,6 +7,7 @@
 import csv
 import threading
 import hashlib
+from typing import List
 import json
 import datetime
 import zipfile
@@ -27,7 +28,15 @@
 from src.utils.resources import SharedResources
 
 
-def get_available_cloud_models_list():
+def get_available_cloud_models_list() -> List[List[str]]:
+    """
+    Collects a csv file from Google Drive, summarizing all available models.
+
+    Returns
+    ------
+    List of all available models on the cloud, each expressed as a List[str].
+    Each model list element corresponds to the following headers: Item,link,dependencies,sum.
+    """
     cloud_models_list = []
     # cloud_models_list_url = 'https://drive.google.com/uc?id=1wVjqpQ7S3xTcNJyV2Sp_hSyKglcxfQLe'
     cloud_models_list_url = 'https://drive.google.com/uc?id=1uibFBPBQywX7EGK5G_Oc6CXlDSiOePKF'
@@ -56,6 +65,19 @@ def download_cloud_model_thread(selected_model):
 
 
 def download_cloud_model(selected_model):
+    """
+    Legacy, but still needed, model download method (use recursively from within the DownloadWorker thread.
+    @TODO. Should be removed and the recursive download should just happen inside the worker.
+
+    Parameters
+    ----------
+    selected_model: str
+        Unique name identifier of the model to be downloaded.
+
+    Returns
+    -------
+    Boolean to indicate if the download operation succeeded or failed.
+    """
     model_url = ''
     model_dependencies = []
     model_checksum = None
@@ -126,9 +148,10 @@ def download_cloud_model(selected_model):
 
 def check_local_model_for_update(selected_model):
     """
+    Compares the existing local model with the remote ones, to identify if a new version is available for download,
+    by checking the checksums.
+
 
-    :param selected_model:
-    :return:
     """
     model_url = ''
     model_dependencies = []
@@ -263,7 +286,6 @@ class DownloadWorker(qt.QObject): #qt.QThread
 
     def __init__(self):
         super(qt.QObject, self).__init__()
-        # self.finished_signal = qt.Signal(bool) #WorkerFinishedSignal() #qt.Signal() #qt.Signal(name='workerFinished')
 
     def onWorkerStart(self, model=None, diagnosis=None, docker_image=None):
         try:

Raidionics/Raidionics/src/utils/resources.py

@@ -73,6 +73,7 @@ def set_environment(self):
         self.global_active_model_update = False
 
     def __set_runtime_parameters(self):
+        # Most likely deprecated, as we moved from the seg backend to the rads one!
         # Set of variables sent to the docker images as runtime config, manually chosen by the user.
         self.user_configuration = configparser.ConfigParser()
         self.user_configuration['Predictions'] = {}
@@ -94,6 +95,3 @@ def __set_runtime_parameters(self):
         self.user_diagnosis_configuration['Neuro']['tumor_segmentation_filename'] = ''
         self.user_diagnosis_configuration['Neuro']['brain_segmentation_filename'] = ''
         self.user_diagnosis_configuration['Neuro']['tumor_type'] = ''
-        # @TODO. Give the option to the user to decide what to include in the standardized report generation
-        self.user_diagnosis_configuration['Neuro']['compute_cortical_structures'] = 'True'
-        self.user_diagnosis_configuration['Neuro']['compute_subcortical_structures'] = 'True'