Merge branch 'master' into 'marge'

autotuning/autotuning.py

@@ -45,7 +45,7 @@ def findPort(self):
                 arduino_port = port.device
 
         if arduino_port is None:
-            print("\nNo Arduino found for " + self.name)
+            print("WARNING: No Arduino found for " + self.name)
             return False
         else:
             return arduino_port
@@ -62,7 +62,7 @@ def connect(self):
                 return False
             else:
                 self.device = serial.Serial(port=self.port, baudrate=self.baudrate, timeout=self.timeout)
-                print("\nConnected to Arduino for " + self.name)
+                print("Connected to Arduino for " + self.name)
                 time.sleep(1.0)
 
     def disconnect(self):
@@ -71,7 +71,7 @@ def disconnect(self):
         """
         if self.device is not None:
             self.device.close()
-            print("\nDisconnected from Arduino for " + self.name)
+            print("Disconnected from Arduino for " + self.name)
             self.device = None
 
     def send(self, data):
@@ -123,10 +123,10 @@ def connect(self):
                 time.sleep(0.1)
                 self.device = Hardware.get_VNA(self.interface)
                 self.frequencies = np.array(self.device.readFrequencies()) * 1e-6  # MHz
-                print("\nConnected to nanoVNA for auto-tuning")
+                print("Connected to nanoVNA for auto-tuning")
                 return True
             except:
-                print("\nNo nanoVNA detected for auto-tuning")
+                print("WARNING: No nanoVNA detected for auto-tuning")
                 return False
 
     def getFrequency(self):

autotuning/autotuning_arduino/autotuning_arduino.ino.copy

@@ -1,7 +1,10 @@
-// Code to control the autotuning circuit with python.
-//  cPins[] = {S1, S2, S3, S4, S5, T1, T2, T3, T4, T5, M1, M2, M3, M4, M5, TTL}
-int cPins[] = {23, 31, 29, 27, 25, 41, 39, 37, 35, 33, 43, 51, 49, 47, 45, 53};
-int nPins = 16;
+/* Code to control the autotuning circuit with python.
+We added two relays to control the VNA. First one selects if the autotuning is connected to the scanner or to the VNA.
+Second one switches on or off the VNA to prevent noise coupling to the RF chain in the scanner.
+*/
+//  cPins[] = {S1, S2, S3, S4, S5, T1, T2, T3, T4, T5, M1, M2, M3, M4, M5, VNA, VNA}
+int cPins[] = {34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 51, 53, 47, 49, 43, 45,  32};
+int nPins = 17;
 
 void setup() {
   // Start the Serial communication

configs/hw_config.py

@@ -10,7 +10,6 @@
 import numpy as np
 
 gFactor = [0.025, 0.040, 0.035] # (X, Y, Z) in T/m/o.u.
-max_grad = 80  # mT/m
 max_slew_rate = 50e-3  # mT/m/ms
 grad_raster_time = 30e-6  # s
 grad_rise_time = 400e-6 # s, time for gradient ramps
@@ -29,16 +28,21 @@
 adcFactor = 13.788 # mV/adcUnit
 scanner_name = "Physio V1.01"
 antenna_dict = {"RF01": np.pi/(0.3*70), "RF02": np.pi/(0.3*70)}
+reference_time = 70  # us, reference excitation time to get the amplitude for rabi
 fov = [20.0, 20.0, 20.0]
 dfov = [0.0, 0.0, 0.0]
 bash_path = "D:\Git\git-bash.exe" # use "gnome-terminal" for genome linux
 rp_ip_address = "192.168.5.20"
 rp_version = "rp-122"
+rp_max_input_voltage = 225  # mV
 lnaGain = 50 # dB
+rf_min_gain = 50  # dB  if your rf chain uses a fix gain, set this number equal to lnaGain
+rf_max_gain = 76  # dB, if your rf chain uses a fix gain, set this number equal to lnaGain
 temperature = 293 # k
 shimming_factor = 1e-5
 rx_channels = 4
 
 # Arduinos
 ard_sn_autotuning = '242353133363518050E0'
 ard_sn_interlock = '242353133363518050E1'
+ard_sn_attenuator = '242353133363518050E2'

configs/sys_config.py.copy

@@ -2,4 +2,3 @@ study_case = ["Phantom", "Hand", "Wrist", "Forearm", "Elbow", "Foot", "Ankle", "
 projects = ["None", "La Fe", "Ana Ferri"]
 side = ["Left", "Right"]
 orientation = ["Supine", "Prono"]
-screenshot_folder = "experiments/screenshots"

controller/controller_console.py

@@ -4,7 +4,7 @@
 :affiliation: MRILab, i3M, CSIC, Valencia, Spain
 
 """
-
+import datetime
 import sys
 from PyQt5.QtCore import QObject, pyqtSignal, pyqtSlot
 from widgets.widget_console import ConsoleWidget
@@ -28,17 +28,51 @@ class ConsoleController(ConsoleWidget):
     def __init__(self):
         super().__init__()
 
-    def setup_console(self):
         # Redirect the output of print to the console widget
         sys.stdout = EmittingStream(textWritten=self.write_console)
 
     def write_console(self, text):
         cursor = self.console.textCursor()
         cursor.movePosition(cursor.End)
-        cursor.insertText(text)
+
+        # Get the current time and format it
+        current_time = datetime.datetime.now().strftime("%H:%M:%S")
+        current_time = "<b>" + current_time + "</b>"
+
+        # Give format to the text
+        if "ERROR" in text:
+            text = f'<span style="color:red;"><b>ERROR</b></span>{text[5:]}'
+
+        if "WARNING" in text:
+            text = f'<span style="color:orange;"><b>WARNING</b></span>{text[7:]}'
+
+        if "READY" in text:
+            text = f'<span style="color:green;"><b>READY</b></span>{text[5:]}'
+
+        # Prepend the time to the text
+        if text == "\n" or text == " ":
+            formatted_text = text
+        else:
+            formatted_text = f"{current_time} - {text}"
+            formatted_text = formatted_text.replace("\n", "<br>")
+
+        # Check if the text contains a marker for bold formatting
+        if "<b>" in formatted_text and "</b>" in formatted_text:
+            # Insert the text as HTML to allow formatting
+            cursor.insertHtml(formatted_text)
+        else:
+            # Insert plain text
+            cursor.insertText(formatted_text)
+
         self.console.setTextCursor(cursor)
         self.console.ensureCursorVisible()
 
+    def clear_console(self):
+        """
+        Clear the console widget by removing all its contents.
+        """
+        self.console.clear()  # Clears the console content
+
 class EmittingStream(QObject):
     """
     Emitting stream class.

controller/controller_figures.py

@@ -34,7 +34,7 @@ def wellcomeMessage():
         Note:
             The method does not return any value.
         """
-        print("\nGraphical User Interface for MaRCoS")
+        print("Graphical User Interface for MaRCoS")
         print("J.M. Algarín, PhD")
         print("[email protected]")
         print("mriLab @ i3M, CSIC, Valencia, Spain")

controller/controller_history_list.py

@@ -20,6 +20,7 @@
 from widgets.widget_history_list import HistoryListWidget
 from manager.dicommanager import DICOMImage
 import numpy as np
+import configs.hw_config as hw
 
 
 class HistoryListController(HistoryListWidget):
@@ -53,14 +54,16 @@ def __init__(self, *args, **kwargs):
         self.itemChanged.connect(self.main.sequence_list.updateSequence)
         self.itemEntered.connect(self.main.sequence_list.updateSequence)
 
+    def delete_items(self):
+        while self.count() > 0:
+            self.deleteTask(item_number=0)
+
     def showContextMenu(self, point):
         """
         Displays a context menu at the given point.
 
         :param point: The position where the context menu should be displayed.
         """
-        # Send printed text to the corresponding console
-        self.main.console.setup_console()
 
         self.clicked_item = self.itemAt(point)
         if self.clicked_item is not None:
@@ -87,13 +90,24 @@ def openPostGui(self):
         self.main.post_gui.showMaximized()
         self.main.post_gui.toolbar_image.rawDataLoading(file_path=path + "/mat/", file_name=item_name)
 
-    def deleteTask(self):
+    def deleteTask(self, item_number=None):
         """
         Deletes the currently selected task from the list.
 
         This method removes the currently selected task item from the list widget.
         """
-        self.takeItem(self.row(self.currentItem()))
+        if item_number is None:
+            item = self.currentItem()
+        else:
+            item = self.item(item_number)
+        text = item.text()
+        text = text.split(".", maxsplit=2)
+        key = text[0] + "." + text[1]
+        self.takeItem(self.row(item))
+        if key in self.pending_inputs.keys():
+            self.pending_inputs.pop(text)
+        if key in self.inputs.keys():
+            self.inputs.pop(key)
 
     def addNewFigure(self):
         """
@@ -177,7 +191,7 @@ def addFigure(self):
                 label.setText(self.labels[n])
                 self.main.figures_layout.addWidget(label, row=1, col=col)
                 self.main.figures_layout.addWidget(image, row=2, col=col)
-                self.main.figures_layout.addWidget(sub_label, row=0, col=0, colspan=col+1)
+                self.main.figures_layout.addWidget(sub_label, row=0, col=0, colspan=col + 1)
             except:
                 pass
             n += 1
@@ -196,8 +210,6 @@ def updateHistoryTable(self, item):
 
         :param item: The selected item from which to retrieve the corresponding input data.
         """
-        # Send printed text to the corresponding console
-        self.main.console.setup_console()
 
         # Get the corresponding key to get access to the history dictionary
         item_time = item.text().split(' | ')[0]
@@ -237,8 +249,6 @@ def updateHistoryFigure(self, item):
 
         :param item: The selected item from which to retrieve the corresponding output information.
         """
-        # Send printed text to the corresponding console
-        self.main.console.setup_console()
 
         # Get the corresponding key to get access to the history dictionary
         item_time = item.text().split(' | ')[0]
@@ -257,7 +267,6 @@ def updateHistoryFigure(self, item):
                 sequence.rotations = rotations.copy()
                 sequence.dfovs = shifts.copy()
                 sequence.fovs = fovs.copy()
-            print("\nReference system fixed to image %s" % self.current_output)
         except:
             pass
 
@@ -326,20 +335,31 @@ def waitingForRun(self):
                     seq_name = self.pending_inputs[key][1][0]
                     sequence = copy.copy(defaultsequences[seq_name])
 
-                    # Modify input parameters of the sequence
+                    # Modify input parameters of the sequence according to current item
                     n = 0
                     for keyParam in sequence.mapKeys:
                         sequence.mapVals[keyParam] = self.pending_inputs[key][1][n]
                         n += 1
 
+                    # Specific tasks for calibration
+                    if "Calibration" in key:
+                        if seq_name == 'Larmor':
+                            sequence.mapVals['larmorFreq'] = hw.larmorFreq
+                            try:
+                                sequence.mapVals['shimming'] = defaultsequences['Shimming'].mapVals['shimming']
+                            except:
+                                pass
+                        if seq_name == 'RabiFlops':
+                            sequence.mapVals['shimming'] = defaultsequences['Shimming'].mapVals['shimming']
+
                     # Run the sequence
                     key_index = keys.index(key)
                     raw_data_name = key.split('|')[1].split(' ')[1]
                     output = self.runSequenceInlist(sequence=sequence, key=key, raw_data_name=raw_data_name)
                     if output == 0:
                         # There is an error
                         del self.pending_inputs[key]
-                        print("\n" + key + " sequence finished abruptly with error.")
+                        print("ERROR: " + key + " sequence finished abruptly with error.\n")
                     else:
                         # Add item to the history list
                         file_name = sequence.mapVals['fileName']
@@ -351,7 +371,7 @@ def waitingForRun(self):
                         # Delete outputs from the sequence
                         sequence.resetMapVals()
                         # self.main.sequence_list.updateSequence()
-                        print("\n" + key + " ready!")
+                        print("READY: " + key + "\n")
                     time.sleep(0.1)
                 # Enable acquire button
                 if self.main.toolbar_marcos.action_server.isChecked():
@@ -389,13 +409,21 @@ def runSequenceInlist(self, sequence=None, key=None, raw_data_name=""):
         self.fovs[key] = sequence.fovs.copy()
 
         # Create and execute selected sequence
-        if sequence.sequenceRun(0, self.main.demo):
-            pass
-        else:
+        try:
+            if sequence.sequenceRun(0, self.main.demo):
+                pass
+            else:
+                return 0
+        except Exception as e:
+            print(f"An error occurred in sequenceRun method: {e}")
             return 0
 
         # Do sequence analysis and get results
-        return sequence.sequenceAnalysis()
+        try:
+            return sequence.sequenceAnalysis()
+        except Exception as e:
+            print(f"An erro ocurred in sequenceAnalysis method: {e}")
+            return 0
 
 
 class HistoryListControllerPos(HistoryListWidget):
@@ -535,7 +563,7 @@ def addFigure(self):
                 label = QLabel(self.labels[n])
                 label.setAlignment(QtCore.Qt.AlignCenter)
                 label.setStyleSheet("background-color: black;color: white")
-                self.main.image_view_widget.addWidget(label, row=2*(idx//4)+1, col=idx%4)
+                self.main.image_view_widget.addWidget(label, row=2 * (idx // 4) + 1, col=idx % 4)
 
                 # Figure
                 image2show, x_label, y_label, title = self.main.toolbar_image.fixImage(self.figures[n],
@@ -545,9 +573,9 @@ def addFigure(self):
                                        x_label=x_label,
                                        y_label=y_label,
                                        title=title)
-                self.main.image_view_widget.addWidget(image, row=2*(idx//4)+2, col=idx%4)
+                self.main.image_view_widget.addWidget(image, row=2 * (idx // 4) + 2, col=idx % 4)
 
-                ncol = np.max([ncol, idx%4+1])
+                ncol = np.max([ncol, idx % 4 + 1])
                 self.main.image_view_widget.addWidget(sub_label, row=0, col=0, colspan=ncol)
             except:
                 pass
@@ -575,7 +603,6 @@ def addNewItem(self, image_key=None, stamp=None, image=None, orientation=None, o
             self.operations_hist[self.image_key] = operations
         self.main.image_view_widget.image_key = self.image_key
 
-
         # Update the space dictionary
         self.space[self.image_key] = space
 
@@ -588,8 +615,6 @@ def updateHistoryFigure(self, item):
         Args:
             item (QListWidgetItem): The selected item in the history list.
         """
-        # Send printed text to the corresponding console
-        self.main.console.setup_console()
 
         image_key = item.text()
         if image_key in self.image_hist.keys():
@@ -650,8 +675,6 @@ def updateHistoryTable(self, item):
         Args:
             item (QListWidgetItem): The selected item in the history list.
         """
-        # Send printed text to the corresponding console
-        self.main.console.setup_console()
 
         # Clear the methods_list table
         self.main.methods_list.setText('')
@@ -724,7 +747,7 @@ def deleteSelectedItem(self):
 
         if selected_item.text() in self.image_hist:
             del self.image_hist[selected_item.text()]
-            
+
         if selected_item.text() in self.operations_hist:
             del self.operations_hist[selected_item.text()]