pySPEC Support
Note that most insctructions are from Esben Rossels pyCCDGUI.
The pySPEC Help & Support page provides clear setup guides, troubleshooting steps, and a detailed user manual. Learn how to connect your spectrometer, adjust exposure settings, analyze spectra, and resolve common issues for smooth, reliable operation of your pySPEC app.
Communication device
The communication device is the identifier for the USB->serial connection. The label under the entrybox states if the given device is accessible or not. Beware that the label only updates during startup and editing of the entry. If the Nucleo is attached after starting the application, the label may or may not be correct.
If a valid device is not selected, an error message will appear when pressing Collect.
Linux
On Linux the STM32 Nucleo board attaches as a tty-device. The default on Debian-based systems is:
/dev/ttyACM0
If the Nucleo does not attach as the default device, check the output of dmesg or the contents of /dev/.
You may find that the device exists, but you still get an error message when pressing collect. This is likely a permission problem. It can be solved by adding your user to the dialout group. Type:
sudo adduser esben dialout
macOS
On macOS the STM32 Nucleo board attaches itself as a device called:
/dev/cu.usbmodemXYZ
Check the contents of /dev/ to find out what to replace XYZ with. In case this directory is hidden from view in Finder, open a terminal and type:
ls /dev/
Windows
Windows uses an entirely different subsystem for serial communication than *NIX systems. The STM32 Nucleo is attached as a COM port (if the STM32 Virtual COM port driver is installed). Try with:
COMn
Where n is an integer, e.g. COM6.
Driving pulses
The TCD1304 requires 3 driving pulses:
MCLK (master clock)
SH (shift gate)
ICG (integration clear gate)
The following is for STM32F40x firmwares. If you use the STM32F103 make sure to also read the final paragraph.
MCLK – The master clock
The MCLK (sometimes called fM or φM) is the CCD’s clock speed. It defines the time-base which the TCD1304 operates in, and for the unmodified CCD driver firmware MCLK has the value:
MCLK = 2.0 MHz
The value of MCLK is used to derive the integration time from the SH pulse.
SH – The shift gate
The SH pulse defines the integration time (tint), which for the TCD1304 cannot be shorter than 10 µs. The user controls the SH period, which together with MCLK, determines the frequency of the SH pulse:
SH-frequency = MCLK / SH-period
tint = 1 / SH-frequency = SH-period / MCLK
Because the CCD has a minimum integration time of 10 µs, the SH period cannot be smaller than:
SH-period = tint × MCLK = 10 µs × 2.0 MHz = 20
Because the timer controlling SH is 32-bit, the largest value for SH-period is
2³² – 1 = 4294967295
Corresponding to a maximum integration time of
tint = (2³² – 1) / 2.0 MHz = 35 min
Example:
Say one wishes to make a collection with an integration time of 15 ms. Then:
SH-period = tint × MCLK = 15 ms × 2.0 MHz = 30000
ICG – The integration clear gate
The ICG pulse defines the moment when the pixels are dumped to the output pin. The ICG pulse must coincide with an SH pulse:
ICG-period = n × SH-period
where n is an integer. When n = 1, the CCD is in normal mode. When n > 1, it runs in electronic shutter mode.
Because it takes 4 MCLK cycles to output 1 pixel, and the chip has 3694 pixels, the minimum ICG-period is
4 × 3694 = 14776
This defines the readout time:
tread = 14776 / 2.0 MHz = 7.4 ms
In the unmodified firmware, the user LED blinks at half the ICG frequency.
STM32F103 specifics
MCLK = 800 kHz
Since timers are 16-bit, max SH/ICG = 65535
tint = 65535 / 800 kHz = 82 ms
Minimum ICG = 14776
Minimum SH = 10 µs × 800 kHz = 8
Single
MCU returns one dataset. If averaging is enabled, collects n times then averages.
Continuous
MCU reads CCD continuously, returning datasets at a rate determined by ICG and averaging.
Settings can’t be changed during continuous capture.
Important
The MCU can read faster than it can transmit, so care must be taken.
UART (STM32F401)
UART is slow (~641 ms per transfer).
ICG-period should be at least:
ICG > 641 ms × 2.0 MHz = 1.282 × 10⁶
USB (STM32F103 / STM32F405)
USB is faster (12 Mbps max theoretical).
STM32F103
Continuous mode works with ICG ≥ 44000 and averaging = 2.
Max FPS:
fps = 800 kHz / (2 × 42000) = 9.5 Hz
Keep ICG ≥ 32000 to allow for averaging overhead.
Averaging
S/N may be increased by collecting n identical recordings and averaging them to cancel out noise. In theory, signal improves by √n.
However, CCDs are subject to readout noise, so it may be preferable to collect a single recording with longer integration time.
The firmware supports onboard averaging (2–15 recordings) without requiring multiple transmissions.
Storing individual recordings takes time, so averaging requires a longer ICG-period.
STM32F40x:
ICG-period = n × SH-period ≥ 30000
for MCLK = 2.0 MHz
STM32F103:
ICG-period = n × SH-period ≥ 32000
for MCLK = 800 kHz.
Plot raw data
Pixel potential is inversely related to light intensity, so collected data should be inverted:
Ipixel = 4095 – ADCpixel
Including dark current:
Ipixel = ADCdark – ADCpixel
Dark current is taken from dummy pixels.
By default, the app plots Ipixel (second equation).
Checking “Plot raw data” plots ADCpixel directly.
Only raw data is saved; it’s up to the user to process it elsewhere.
Balanced output
Odd and even pixels use separate output registers, which can cause imbalance.
When “Balanced output” is enabled, the app estimates and corrects this imbalance (RI):
RI = (Σ[even] – Σ[odd]) / 16
Only raw data is saved; correction applies to plotting only.
Mirror data
Mirrors the input along the y-axis to allow for upside down placement of the Sensor.
Show Colours
Only works in Spectroscopy mode. Shows the VIS Colour for the corresponding wavelenght.
Saving files
When saving, raw CCD data is written in a gnuplot-compatible format:
Lines 1–3: general info
Line 4: CCD settings
Lines 5–3698: pixel data
Example:
#Data from the TCD1304 linear CCD
#column 1 = pixelnumber, column 2 = pixelvalue
#Pixel 1–32 and 3679–3694 are dummy pixels
#SH-period: 40 ICG-period: 20000 Integration time: 20 µs
1 3936
2 3934
..
3694 3934
Raw data is saved. Intensities are computed as
Ipixel = ADCdark – ADCpixel
Dark current comes from dummy pixels.
Opening files
The app expects the same data format as above.
CLI data is identical, so files from the command-line version can be opened directly.
Regression and Regression strength
If toggled, calculates an aproximate function through a list of points given by the data input. This helps reduce noise and can apporximate the real graph based on the condition of the raw data graph.
Raw Opacity
Was implemented to allow for better seeing of the regression. Can be toggled without using regression aswell.
