Add help menu with documentation and ... help

cpdctrl_gui/main.py

@@ -1,3 +1,4 @@
+import os
 import sys
 if __name__ == "__main__":
     if __package__ is None:
@@ -14,5 +15,4 @@ from cpdctrl_gui import init
 
 if __name__ == '__main__':
     import sys
-
+    sys.exit(init.run())
-    sys.exit(init.run())

cpdctrl_gui/resources/about.md

@@ -1,4 +1,5 @@
 ## About 
+`cpdctrl-gui` is a program for conducting contact potential difference (CPD) measurements under illumination.
 
 - Author: Matthias Quintern
 - License: [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html)

cpdctrl_gui/resources/data_recording.md

@@ -0,0 +1,15 @@
+## Data recording
+
+### Buffer mode
+**TODO**
+
+### Data flushing
+Measurements can be performed over many hours or multiple days.
+To make sure that unforeseen accidents like Windows Updates do not ruin the entire measurement,
+the data can be continuously written to the disk.  
+To enable this feature, set `Flush After` to a non-zero value (in the Measurement Settings tab).
+After \<Flush After\> number of datapoints are recorded, they are written to the cache directory
+as serialized numpy array.
+When the measurement is finished, all partial arrays are loaded again and the complete data 
+can be saved as `csv` or serialized numpy array (`.pkl`).
+

cpdctrl_gui/resources/led_control.md

@@ -0,0 +1,42 @@
+## LED Control
+To automatically control the LED state during the measurement, you can 
+use a LED script.
+The LED script is a simple text file with lines in this format:  
+`<duration> <led state>`  
+The script starts at the top, applies `<led state>` for `<duration>` and moves to the next line.
+
+- `<duration>`: Integer, time in seconds. Alternatively, you may append `s`, `m` or `h`, for seconds, minutes, hours.
+- `<led state>`: LED brightness in percent. Can be an integer between 0-100 or `on` or `off`. 
+  Numbers between 1-99 may only be used if the LED controller supports that (the Arduino/LEDD1B does not).
+
+Comments may start with `#`. Leading and trailing whitespaces as well as empty lines are ignored.
+
+### Example
+```
+# turn on (100%) for 20 seconds
+20 on
+5 off# comments after statements allowed
+5 100     # whitespace before comments after statements allowed
+# turn off for 5 seconds
+5s 0
+# set to 65% for 1 minute
+1m 65
+# turn off for 1 minute and 10 seconds
+1m10s off
+# turn on off for 1 hour, 5 minutes and 45 seconds
+1h5m45s on
+```
+
+### Live changes
+The script can be adapted during the measurement in two ways:
+First, in the GUI through the table in the `LED Script` tab on the left.
+Second, by modifying the text file that was loaded (requires "Watch LED Script" checkbox to be ticked).
+
+You can:
+- change any LED value
+- change durations of future steps
+- add/remove future lines (currently only by modifying the file)
+
+You can not:
+- change steps from the past 
+- make the current step so short that it would be skipped

cpdctrl_gui/resources/sample_changing.md

@@ -0,0 +1,42 @@
+## Changing the sample
+1. Stop the turbopump:
+    1. Press the stop button on the control panel
+    2. Close the valve between pump and chamber (on top of the turbo pump), by screwing it into the pump
+2. Ventilate the chamber
+    1. Open the gate valve
+    2. Carefully open the needle valve (usually less than 1/8 turn)
+    3. When the chamber can be moved, close both valves again
+3. Take off the chamber
+    1. Make some space to put the chamber (mind the grease on the bottom edge)
+    2. Carefully lift the chamber. Good places to grab it are the tubing on the left and the right bottom edge.  
+       ***Caution***: The tube connecting the chamber with the pump will exert a force to the right!  
+       **Make sure you do not crash the chamber into the sample tray!**
+4. Move the sample away from the gold mesh
+    1. Move the tray fully down by turning the upper micrometer screw *counterclockwise*
+    2. Move the tray fully to the left using the larger micrometer screw
+    3. Loosen the screw on the clamp holding the sample in place and remove the sample
+5. Prepare the new sample
+    1. Put the sample on the tray and place the clamp on it.
+    2. Tighten the clamp screw (you might need to grab the nut on the bottom side)
+    3. Move the tray in x-position using the large micrometer screw.  
+       The gold mesh should be well aligned with the sample surface
+    4. Carefully move the tray up by turning the small micrometer screw *clockwise*.
+       Leave about half a millimeter of space between the sample and the gold mesh  
+       **Do not crash the sample into the gold mesh!**
+6. Put the chamber back on
+    1. Put the chamber back on and align it on the two posts on the bottom and right
+    2. Check the backside to make sure that no cables are sticking out
+7. Vacuum the chamber
+    1. Make sure the nitrogen venting valves are closed
+    2. **Make sure the turbopump is not spinning anymore**
+    3. When the turbopump has fully stopped, slowly open the valve on top of the pump
+    4. Fully open the valve
+    5. **Wait** until the vacuum is in the lower 1E-2 range, eg 4.0E-2 (read the value from the sensor attached to the turbopump)
+    6. Only when this target pressure is reached, turn on the turbopump (control panel on top shelf)
+    7. Wait until the desired vacuum for measurement is reached (usually 1E-5)
+        - 1E-4: **TODO**
+        - 1E-5: **TODO**
+        - 1E-6: after 1-2 days
+
+       If the pressure does not drop enough: Use isopropanol to inspect for leaks
+

cpdctrl_gui/resources/small_about.md

@@ -0,0 +1,5 @@
+## About
+
+- Author: Matthias Quintern
+- License: [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html)
+- Source Code: https://git.quintern.xyz/MatthiasQuintern/cpdctrl-gui

cpdctrl_gui/resources/technical_information.md

@@ -0,0 +1,23 @@
+## Technical Information
+### cpdctrl-gui Software
+`cpdctrl-gui` is written in python and uses the Qt framework for the graphical user interface.  
+Most functionality like interaction with the various devices is provided by the `cpdctrl` package,
+which can be used without the GUI in an ipython shell for advanced or debugging purposes.
+
+
+
+### Arduino Code
+To control the ThorLabs LEDD1B, it is connected to an Arduino Nano, which is connected to the lab PC
+via USB. The Arduino must have the correct software loaded in order to communicate with `cpdctrl` and the LEDD1B.
+1. Open the Arduino IDE
+2. Open the sketch `~/cpd-dev/cpdctrl/arduino-thorlabs-led/led_control/led_control.ino`
+3. Select `COM4` and `Arduino Nano` and then 'Upload Sketch'
+
+### CPD Controller Calibration
+**TODO**
+This process is not always necessary.
+1. Set CPD Controller to Manual, Offset=Gold Work Function, Filter off (so you can see what happens immediately), Oscillator to ~2
+2. Move the micrometer screw close until a signal appears
+3. Set Automatic offset so that the output is 0V
+
+

cpdctrl_gui/resources/troubleshooting.md

@@ -1,6 +1,10 @@
 ## Troubleshooting
-### 1) The LED does not work
+### 1) General
+The program writes information to a log file, which might contain helpful information.
+It is located in the cache directory, usually in `~/.cache/cpdctrl-gui`.
+
+### 2) The Arduino/LEDD1B does not work
 1) Make sure the Thorlabs LED is plugged in, turned on (turn the dial to a non-zero value) and that the switch is in the **TRIG**er position
 2) Reset the Arduino by pressing the white button on the top and restart the program
 3) Unplug and replug the Arduino and restart the program
-4) Re-upload the code (see section "Arduino Code")
+4) Re-upload the code (see section "Technical Information/Arduino Code")

cpdctrl_gui/resources/user_guide.md

@@ -1,54 +1 @@
-# CPD User Guide
+## User Guide
-## Changing the sample
-1. Stop the turbopump:
-   1. Press the stop button on the control panel
-   2. Close the valve between pump and chamber (on top of the turbo pump), by screwing it into the pump
-2. Ventilate the chamber
-   1. Open the gate valve
-   2. Carefully open the needle valve (usually less than 1/8 turn)
-   3. When the chamber can be moved, close both valves again
-3. Take off the chamber
-   1. Make some space to put the chamber (mind the grease on the bottom edge)
-   2. Carefully lift the chamber. Good places to grab it are the tubing on the left and the right bottom edge.  
-      ***Caution***: The tube connecting the chamber with the pump will exert a force to the right!  
-      **Make sure you do not crash the chamber into the sample tray!**
-4. Move the sample away from the gold mesh
-   1. Move the tray fully down by turning the upper micrometer screw *counterclockwise*
-   2. Move the tray fully to the left using the larger micrometer screw
-   3. Loosen the screw on the clamp holding the sample in place and remove the sample
-5. Prepare the new sample
-   1. Put the sample on the tray and place the clamp on it.
-   2. Tighten the clamp screw (you might need to grab the nut on the bottom side)
-   3. Move the tray in x-position using the large micrometer screw.  
-      The gold mesh should be well aligned with the sample surface 
-   4. Carefully move the tray up by turning the small micrometer screw *clockwise*.
-      Leave about half a millimeter of space between the sample and the gold mesh  
-      **Do not crash the sample into the gold mesh!**
-6. Put the chamber back on
-   1. Put the chamber back on and align it on the two posts on the bottom and right
-   2. Check the backside to make sure that no cables are sticking out
-7. Vacuum the chamber
-   1. Make sure the nitrogen venting valves are closed
-   2. **Make sure the turbopump is not spinning anymore**
-   3. When the turbopump has fully stopped, very slowly open the valve on top of the pump
-   4. Fully open the valve **TODO: hier noch irgendwelche checks?**
-   5. **Wait** until the vacuum is in the lower $10^{-2}$ range (read the value from the sensor attached to the turbopump)
-   6. Only when this target pressure is reached, turn on the turbopump (control panel on top)
-   7. Wait until the desired vacuum for measurement is reached (usually $10^{-5}$)
-      - $10^{-4}$: **TODO**
-      - $10^{-5}$: **TODO**
-      - $10^{-6}$: after 1-2 days 
-      
-      If the pressure does not drop enough: Use isopropanol to inspect for leaks
-
-## CPD Controller Calibration
-**TODO**
-
-This process is not always necessary.
-1. Set CPD Controller to Manual, Offset=Gold Work Function, Filter off (so you can see what happens immediately), Oscillator to ~2
-2. Move the micrometer screw close until a signal appears
-3. Set Automatic offset so that the output is 0V
-Calibration: Fresh graphite probe
-
-## cpdctrl-gui Software
-**TODO**

cpdctrl_gui/ui/main_window.py

@@ -5,9 +5,10 @@ from PyQt6.QtCore import Qt, QTimer, QFileSystemWatcher
 from PyQt6.QtWidgets import QMainWindow, QWidget, QHBoxLayout, QLabel, QStatusBar, QFileDialog, \
     QVBoxLayout
 from PyQt6.QtWidgets import QTabWidget
-from PyQt6.QtGui import QIcon, QPixmap, QAction, QKeySequence, QDragEnterEvent
+from PyQt6.QtGui import QIcon, QAction, QKeySequence, QDragEnterEvent
 from PyQt6.QtWidgets import QDialog, QDialogButtonBox, QMessageBox
 
+from .widgets.help import HelpMenu
 from ..resources import get_resource_path
 from .widgets.menubar import MenuBar
 from .widgets.toolbar import ToolBar
@@ -15,8 +16,9 @@ from .widgets.metadata_input import MetadataInput
 from cpdctrl_gui.ui.widgets.settings import MeasurementSettings, AppSettings
 from .widgets.plot import Plot
 from .widgets.device_select import ListChoice
-from .widgets.about import MarkdownView
+from .widgets.about import About
 from .widgets.led_script import LedScriptViewer
+from .widgets.help import HelpMenu
 # from .widgets.treeview import TreeView
 
 import time
@@ -332,7 +334,6 @@ class MainWindow(QMainWindow):
             raise RuntimeError("No led control device selected")
         self.idle_stop()
 
-        raise KeyError("Exception for testing")
         name = self.w_measurement_settings.get_value("name")
         script = self.w_measurement_settings.get_value("led_script")
         flush_after = self.w_measurement_settings.get_value("flush_after")
@@ -615,17 +616,7 @@ class MainWindow(QMainWindow):
         buttons = QDialogButtonBox(QDialogButtonBox.StandardButton.Ok)
         buttons.accepted.connect(dialog.accept)
         dialog.setLayout(QVBoxLayout())
-        # show the logo via a pixmap in a label
+        dialog.layout().addWidget(About())
-        img_path = get_resource_path("icons/logo.svg")
-        pixmap = QPixmap(img_path)
-        pixmap = pixmap.scaled(128, 128, Qt.AspectRatioMode.KeepAspectRatio, Qt.TransformationMode.SmoothTransformation)
-        # qt cant find the file
-        label = QLabel()
-        label.setPixmap(pixmap)
-        label.setAlignment(Qt.AlignmentFlag.AlignCenter)  # center the image
-        dialog.layout().addWidget(label)
-        # show about.md
-        dialog.layout().addWidget(MarkdownView("about.md"))
         dialog.layout().addWidget(buttons)
         dialog.exec()
 
@@ -635,9 +626,7 @@ class MainWindow(QMainWindow):
         buttons = QDialogButtonBox(QDialogButtonBox.StandardButton.Ok)
         buttons.accepted.connect(dialog.accept)
         dialog.setLayout(QVBoxLayout())
-        # show help.md
+        dialog.layout().addWidget(HelpMenu())
-        #dialog.layout().addWidget(MarkdownView("troubleshooting.md"))
-        dialog.layout().addWidget(MarkdownView("user_guide.md"))
         dialog.layout().addWidget(buttons)
         # set larger window size
         dialog.resize(800, 600)

cpdctrl_gui/ui/widgets/about.py

@@ -1,5 +1,6 @@
-from PyQt6.QtWidgets import QTextBrowser
+from PyQt6.QtWidgets import QTextBrowser, QWidget, QLabel, QVBoxLayout
-from PyQt6.QtGui import QDesktopServices
+from PyQt6.QtCore import Qt
+from PyQt6.QtGui import QDesktopServices, QPixmap
 
 from ...resources   import get_resource_path
 
@@ -8,19 +9,45 @@ import logging
 log = logging.getLogger(__name__)
 
 class MarkdownView(QTextBrowser):
-    def __init__(self, path):
+    def __init__(self, parent=None):
-        super().__init__()
+        super().__init__(parent)
         self.setReadOnly(True)
-        self.filepath = get_resource_path(path)
-        try:
-            with open(self.filepath, "r") as file:
-                content = file.read()
-                self.setMarkdown(content)
-        except FileNotFoundError:
-            log.error(f"File not found: {self.filepath}")
-            self.setMarkdown(f"## File not found\n`{self.filepath}`")
-
         # open links with the OS web browser
         self.anchorClicked.connect(QDesktopServices.openUrl)
         # dont follow links
         self.setOpenLinks(False)
+
+class About(QWidget):
+    """
+    Small about text with logo
+    """
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setLayout(QVBoxLayout())
+        # show the logo via a pixmap in a label
+        img_path = get_resource_path("icons/logo.svg")
+        pixmap = QPixmap(img_path)
+        pixmap = pixmap.scaled(128, 128, Qt.AspectRatioMode.KeepAspectRatio, Qt.TransformationMode.SmoothTransformation)
+        # qt cant find the file
+        w_label = QLabel()
+        w_label.setPixmap(pixmap)
+        w_label.setAlignment(Qt.AlignmentFlag.AlignCenter)  # center the image
+        self.layout().addWidget(w_label)
+        # show about.md
+        w_md_view = MarkdownView()
+        filepath = get_resource_path("small_about.md")
+        try:
+            with open(filepath, "r") as file:
+                content = file.read()
+                try:
+                    from importlib.metadata import version
+                    cpdversion = version('cpdctrl_gui')
+                    content += f"\n- Version: {cpdversion}"
+                except Exception as e:
+                    log.info(f"Failed to get cpdctrl_gui version: {e}")
+                    # content += f"\n- Version: Unknown"
+                w_md_view.setMarkdown(content)
+        except FileNotFoundError:
+            log.error(f"File not found: {filepath}")
+            w_md_view.setMarkdown(f"## File not found\n`{filepath}`")
+        self.layout().addWidget(w_md_view)

cpdctrl_gui/ui/widgets/help.py

@@ -0,0 +1,49 @@
+from PyQt6.QtWidgets import QWidget, QTextBrowser, QHBoxLayout, QListWidget, QListWidgetItem
+from PyQt6.QtGui import QDesktopServices
+from ...resources import get_resource_path
+from .about import MarkdownView
+
+import logging
+log = logging.getLogger(__name__)
+
+# Ordered list of help files to use
+GUI_FILES = [
+    ("about.md", "About"),
+    ("sample_changing.md", "Changing the Sample"),
+    ("data_recording.md", "Data recording"),
+    ("led_control.md", "LED control"),
+    ("troubleshooting.md", "Troubleshooting"),
+    ("technical_information.md", "Technical Information"),
+]
+
+class HelpMenu(QWidget):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setLayout(QHBoxLayout())
+        self.w_list = QListWidget()
+        self.w_list.setMaximumWidth(200)
+        self.layout().addWidget(self.w_list)
+        self.w_viewer = MarkdownView()
+        self.layout().addWidget(self.w_viewer)
+        files = [(get_resource_path(f), name) for (f,name) in GUI_FILES]
+        for i, (f, name) in enumerate(files):
+            w_item = QListWidgetItem(name)
+            w_item.filepath = f
+            self.w_list.addItem(w_item)
+            if i == 0:
+                self.set_view(w_item)
+                self.w_list.setCurrentRow(0)
+        self.w_list.itemClicked.connect(self.set_view)
+
+    def set_view(self, list_item):
+        try:
+            filepath = list_item.filepath
+            try:
+                with open(filepath, "r") as file:
+                    content = file.read()
+                    self.w_viewer.setMarkdown(content)
+            except FileNotFoundError:
+                log.error(f"File not found: {filepath}")
+                self.w_viewer.setMarkdown(f"## File not found\n`{filepath}`")
+        except AttributeError:
+            log.error(f"Invalid list item")

pyproject.toml

@@ -2,9 +2,9 @@
 requires = ["setuptools"]
 
 [project]
-name = "cpdctrl-gui"
+name = "cpdctrl_gui"
-version = "0.1.0"
+version = "1.0.0"
-description = "GUI Utility for CPD measurements with a Keitley 2700 SMU and an Arduino-controlled light source"
+description = "GUI Utility for CPD measurements with a Keitley 2700 SMU and a controlled light source"
 requires-python = ">=3.10"
 readme = "README.md"
 license = {file = "LICENSE"}