Merge pull request #2 from BritishGeologicalSurvey/concat_sample_name

Update CSV export formatting and scaling usability

README.md

@@ -33,16 +33,17 @@
             User Interface with data preprocessing and data flow
             ---
             +testing_mode: bool
-            +default_settings: dict
+            +default_settings: dict[str, Any]
             +image_filepath: str
             +csv_filepath: str
             +point_colour: str
-            +status_bar_messages: dict
+            +status_bar_messages: dict[str, dict[str, Any]]
             +graphics_view: GraphicsView
             +graphics_scene: GraphicsScene
             +table_model: TableModel
             +table_view: TableView
             +set_scale_dialog: SetScaleDialog
+            +main_input_widgets: list[QWidget]
 
             +setup_ui_elements()
             +set_colour_button_style()
@@ -65,6 +66,7 @@
             +update_analysis_points()
             +set_point_colour()
             +toggle_scaling_mode()
+            +toggle_main_input_widgets(enable)
             +clear_scale_clicked()
             +set_scale(scale)
             +get_point_settings(analysis_point, clicked_column_index)
@@ -155,9 +157,9 @@
             QAbstractTableModel
             Manage AnalysisPoint data
             ---
-            +headers: list
-            +_data: list
-            +editable_columns: list
+            +headers: list[str]
+            +_data: list[list[Any]]
+            +editable_columns: list[int]
 
             +headerData(section, orientation, role)
             +columnCount(*args)

instructions.md

@@ -38,6 +38,8 @@ _Export the current analysis point data to a TACtool CSV file._
 
 By default, the exported file will be a CSV file. However, you can add your own file extension to the filename if you wish to create a different file type, though this is not recommended.
 
+Upon export, the **sample_name** and **id** columns will be concatenated into a single column labeled **Name**, using the character pattern **_#** to join them.
+
 ## User Interface Buttons
 
 ### Clear Points
@@ -84,19 +86,13 @@ _Note: The **Diameter** is measured in **µm**_
 
 ### Scale
 
-The scale can be set in 1 of 2 ways.
-
-**Set Scale Dialog**
+To set the scale, complete the following steps:
 
 - Press the _Set Scale_ button. A _Set Scale_ window will then open.
 - The image on the main window will become slightly grey. This means you can now draw a line across the image. Start by clicking once to create the start of the line and clicking again to create the end of the line. Pressing the _Clear_ button will remove any current lines.
 - Now you change the estimated distance in microns. To do this, either use the up/down arrows next to the _Distance_ input box, or type in your own value. It must be a whole number.
 - Pressing _OK_ will confirm the new scale and close the _Set Scale_ window.
 
-**Directly Setting the Scale Value**
-
-Alternatively, if you already know the scale value you would like to use, you can input this by typing it into the _Scale_ input box on the main window, next to the _Set Scale_ button.
-
 _Note: The **Scale** is measured in **Pixels per µm**_
 
 ## Analysis Points

tactool/set_scale_dialog.py

@@ -39,7 +39,7 @@ def __init__(self, testing_mode: bool) -> None:
 
         # Setting the Dialog Box settings
         self.setWindowTitle("Set Scale")
-        self.setGeometry(0, 50, 100, 200)
+        self.setMinimumSize(100, 200)
         self.setWindowFlags(
             Qt.Window | Qt.WindowCloseButtonHint | Qt.WindowStaysOnTopHint
         )
@@ -60,19 +60,19 @@ def setup_ui_elements(self) -> None:
         self.clear_scale_button = QPushButton("Clear", self)
         self.cancel_button = QPushButton("Cancel", self)
 
+        # Distance label and input
+        distance_label = QLabel("Distance (µm):")
+        self.distance_input = QSpinBox()
+        self.distance_input.setMaximum(100000)
+
         # Pixels label and input
         pixels_label = QLabel("Pixels:")
         self.pixel_input = QLineEdit()
         self.pixel_input.setText(self.pixel_input_default)
         self.pixel_input.setEnabled(False)
 
-        # Distance label and input
-        distance_label = QLabel("Distance (µm):")
-        self.distance_input = QSpinBox()
-        self.distance_input.setMaximum(100000)
-
         # Scale label and input
-        scale_label = QLabel("Scale:")
+        scale_label = QLabel("Scale (Pixels per µm):")
         self.scale_value = QLineEdit()
         self.scale_value.setValidator(QDoubleValidator())
         self.scale_value.setEnabled(False)
@@ -86,10 +86,10 @@ def setup_ui_elements(self) -> None:
 
         # Arrange label and input boxes layout
         settings_widgets_layout = QVBoxLayout()
-        settings_widgets_layout.addWidget(pixels_label)
-        settings_widgets_layout.addWidget(self.pixel_input)
         settings_widgets_layout.addWidget(distance_label)
         settings_widgets_layout.addWidget(self.distance_input)
+        settings_widgets_layout.addWidget(pixels_label)
+        settings_widgets_layout.addWidget(self.pixel_input)
         settings_widgets_layout.addWidget(scale_label)
         settings_widgets_layout.addWidget(self.scale_value)
 

tactool/table_model.py

@@ -9,7 +9,10 @@
 from csv import writer
 from pathlib import Path
 from textwrap import dedent
-from typing import Optional
+from typing import (
+    Any,
+    Optional,
+)
 
 from PyQt5.QtCore import (
     pyqtSignal,
@@ -105,7 +108,7 @@ def __init__(self) -> None:
         super().__init__()
         # Set the headers of the table to be the names of the Analysis Point attributes
         self.headers = AnalysisPoint.field_names()
-        self._data = []
+        self._data: list[list[Any]] = []
         self.editable_columns = [
             self.headers.index("label"),
             self.headers.index("sample_name"),
@@ -292,6 +295,8 @@ def convert_export_headers(self) -> list[str]:
         headers = self.headers[:len(self.headers) - 3]
         for old_header, new_header in zip(header_conversions, header_conversions.values()):
             headers[headers.index(old_header)] = new_header
+        # Remove the sample_name field
+        headers.pop(headers.index("sample_name"))
 
         # Insert a new Z column after the Y column for the laser formatting
         z_index = headers.index("Y") + 1
@@ -303,7 +308,16 @@ def convert_export_point(self, analysis_point: AnalysisPoint) -> list:
         """
         Function to convert an Analysis Point formatting for a CSV export.
         """
+        headers = self.headers[:len(self.headers) - 3]
+        id_idx, sample_name_idx = headers.index("id"), headers.index("sample_name")
         analysis_point_row = analysis_point.aslist()[:len(self.headers) - 3]
-        z_index = self.headers.index("y") + 1
+
+        # Concat the sample_name and id into 1 column
+        # Also pads zeros on id column value
+        analysis_point_row[id_idx] = f"{analysis_point.sample_name}_#{analysis_point.id:03d}"
+        analysis_point_row.pop(sample_name_idx)
+
+        # Insert a new Z column after the Y column for the laser formatting
+        z_index = headers.index("y") + 1
         analysis_point_row.insert(z_index, 0)
         return analysis_point_row

tactool/window.py

@@ -9,9 +9,7 @@
 from textwrap import dedent
 from typing import Optional
 
-from PyQt5.QtCore import (
-    QModelIndex,
-)
+from PyQt5.QtCore import QModelIndex
 from PyQt5.QtGui import QFont
 from PyQt5.QtWidgets import (
     QColorDialog,
@@ -72,6 +70,7 @@ def __init__(self, testing_mode: bool) -> None:
 
         # Setup the User Interface
         self.setWindowTitle("TACtool")
+        self.setMinimumSize(750, 650)
         self.graphics_view = GraphicsView()
         self.graphics_scene = self.graphics_view.graphics_scene
         self.table_model = self.graphics_view.graphics_scene.table_model
@@ -80,6 +79,19 @@ def __init__(self, testing_mode: bool) -> None:
         self.setup_ui_elements()
         self.connect_signals_and_slots()
         self.toggle_status_bar_messages()
+        self.main_input_widgets = [
+            self.menu_bar_file,
+            self.sample_name_input,
+            self.mount_name_input,
+            self.material_input,
+            self.label_input,
+            self.colour_button,
+            self.diameter_input,
+            self.reset_ids_button,
+            self.reset_settings_button,
+            self.clear_points_button,
+            self.table_view,
+        ]
 
 
     def setup_ui_elements(self) -> None:
@@ -122,14 +134,15 @@ def setup_ui_elements(self) -> None:
 
         # Input for point diameter
         diameter_label = QLabel("Diameter (μm):")
-        self.diameter_box = QSpinBox()
-        self.diameter_box.setValue(self.default_settings["diameter"])
-        self.diameter_box.setMaximum(100000)
+        self.diameter_input = QSpinBox()
+        self.diameter_input.setValue(self.default_settings["diameter"])
+        self.diameter_input.setMaximum(100000)
 
         # Input for scaling
         scale_label = QLabel("Scale (Pixels per µm):")
-        self.scale_value = QLineEdit()
-        self.scale_value.setText(self.default_settings["scale"])
+        self.scale_value_input = QLineEdit()
+        self.scale_value_input.setText(self.default_settings["scale"])
+        self.scale_value_input.setDisabled(True)
         self.set_scale_button = QPushButton("Set Scale", self)
 
         # Main buttons
@@ -165,9 +178,9 @@ def setup_ui_elements(self) -> None:
 
         # Scaling widgets
         sidebar.addWidget(diameter_label)
-        sidebar.addWidget(self.diameter_box)
+        sidebar.addWidget(self.diameter_input)
         sidebar.addWidget(scale_label)
-        sidebar.addWidget(self.scale_value)
+        sidebar.addWidget(self.scale_value_input)
         sidebar.addWidget(self.set_scale_button)
         sidebar.addStretch(stretch=6)
 
@@ -246,7 +259,7 @@ def ref_points(self: Window):
             return condition, message
 
         def set_scale(self: Window):
-            condition_1 = self.scale_value.text() == self.default_settings["scale"]
+            condition_1 = self.scale_value_input.text() == self.default_settings["scale"]
             condition_2 = len(self.table_model.reference_points) >= 3
             condition = condition_1 and condition_2
             message = "Have you set a scale?"
@@ -394,6 +407,11 @@ def process_tactool_csv(self, filepath: str) -> None:
             reader = DictReader(csv_file)
             # Iterate through each line in the CSV file
             for id, item in enumerate(reader):
+
+                # Split the id and sample_name value from the Name column
+                if "_#" in item["Name"]:
+                    item["sample_name"], item["Name"] = item["Name"].rsplit("_#", maxsplit=1)
+
                 # The default ID value is incremented with the row number
                 default_values["Name"] = id + 1
                 # If there is a Z column which is requried for the laser, then remove it
@@ -498,7 +516,7 @@ def validate_current_data(self, validate_image: bool = False) -> bool:
                 return False
 
         # If the scale value has not been changed
-        if self.scale_value.text() == self.default_settings["scale"]:
+        if self.scale_value_input.text() == self.default_settings["scale"]:
             message = dedent("""
                 A scale value has not been set.
 
@@ -538,9 +556,9 @@ def add_analysis_point(
             # Get the required input values from the window input settings
             # Coordinates and the Point ID are taken from the arguments, notes defaults to None
             label = self.label_input.currentText()
-            diameter = self.diameter_box.value()
+            diameter = self.diameter_input.value()
             colour = self.point_colour
-            scale = float(self.scale_value.text())
+            scale = float(self.scale_value_input.text())
             sample_name = self.sample_name_input.text()
             mount_name = self.mount_name_input.text()
             material = self.material_input.text()
@@ -681,6 +699,11 @@ def toggle_scaling_mode(self) -> None:
         if self.set_scale_dialog is None:
             # Create the Set Scale Dialog box
             self.set_scale_dialog = SetScaleDialog(self.testing_mode)
+            # Disable main window input widgets
+            self.toggle_main_input_widgets(False)
+            # Move the Set Scale Dialog box to be at the top left corner of the main window
+            main_window_pos = self.pos()
+            self.set_scale_dialog.move(main_window_pos.x() + 50, main_window_pos.y() + 50)
 
             # Connect the Set Scale dialog buttons
             self.set_scale_dialog.set_scale_clicked.connect(self.set_scale)
@@ -691,6 +714,16 @@ def toggle_scaling_mode(self) -> None:
         # Else when the program is in scaling mode, reset the Set Scaling Dialog value
         else:
             self.set_scale_dialog = None
+            # Enable main window widgets
+            self.toggle_main_input_widgets(True)
+
+
+    def toggle_main_input_widgets(self, enable: bool) -> None:
+        """
+        Toggle each of the input widgets in the main window to be enabled or disabled.
+        """
+        for widget in self.main_input_widgets:
+            widget.setEnabled(enable)
 
 
     def clear_scale_clicked(self) -> None:
@@ -707,7 +740,7 @@ def set_scale(self, scale: float) -> None:
         """
         Function to set the scale of the program given when the Set scale button is clicked in the Set Scale dialog box.
         """
-        self.scale_value.setText(str(scale))
+        self.scale_value_input.setText(str(scale))
         self.toggle_status_bar_messages()
 
 
@@ -775,10 +808,10 @@ def update_point_settings(
             self.label_input.setCurrentText(label)
 
         if diameter is not None:
-            self.diameter_box.setValue(diameter)
+            self.diameter_input.setValue(diameter)
 
         if scale is not None:
-            self.scale_value.setText(str(scale))
+            self.scale_value_input.setText(str(scale))
             self.toggle_status_bar_messages()
 
         if colour is not None:

test/data/analysis_points_complete.csv

@@ -1,6 +1,6 @@
-Name,Type,X,Y,diameter,scale,colour,sample_name,mount_name,material,notes
-1,RefMark,472,336,10,1,#ffff00,sample_x83,mount_x81,rock,
-2,RefMark,394,318,10,1,#ffff00,sample_x83,mount_x81,rock,
-3,RefMark,469,268,10,1,#ffff00,sample_x83,mount_x81,rock,point3
-4,Spot,527,340,10,1,#204a87,sample_x67,mount_x15,duck,"point4 with whitespace, and comma"
-5,Spot,362,380,15,1,#204a87,sample_x67,mount_x15,duck,point5 with whitespace
+Name,Type,X,Y,diameter,scale,colour,mount_name,material,notes
+sample_x83_#001,RefMark,472,336,10,1,#ffff00,mount_x81,rock,this point has padded zeros in the id column
+sample_x83_#2,RefMark,394,318,10,1,#ffff00,mount_x81,rock,
+sample_x83_#3,RefMark,469,268,10,1,#ffff00,mount_x81,rock,point3
+sample_x67_#4,Spot,527,340,10,1,#204a87,mount_x15,duck,"point4 with whitespace, and comma"
+sample_x67_#5,Spot,362,380,15,1,#204a87,mount_x15,duck,point5 with whitespace