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Ulm-IQO / qudi-iqo-modules

A collection of qudi measurement modules originally developed for experiments on colorcenters in semiconductor materials.
GNU General Public License v3.0
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[Bug] config option error using a NI scanner with two AO outputs (2D scanning only) #170

Open syim70 opened 3 weeks ago

syim70 commented 3 weeks ago

Version

current main

What is affected by the bug?

I tried to use a NI scanner with two AO outputs, but config file's scanner gui option "optimizer_plot_dimensions: [2]" does not work. It seems like Qudi requires "z axis" even if there is no additional AO.

When does the bug occur?

  1. Latest release (both qudi-core and qudi-iqo-modules): "optimizer_plot_dimensions: [2]" is not working even with scanner_dummy.
  2. Optimizer_fix_1D branch (#155): "optimizer_plot_dimensions: [2]" is working with scanner_dummy, but not with a real hardware (NI DAQ with two AOs).

How do we replicate the issue?

If users choose only 2D scanning, ni scanner (or optimizer) should not require more axes.

Expected behavior

Please, let me have an options in config file with 2D scanning only.

Relevant log output

No response

Additional Comments

No response

Contact Details

timoML commented 3 weeks ago

Can you please paste the full error that you experience with #155 and nicard? The branch name should be "1d_scanner_optimize".

syim70 commented 3 weeks ago

As you noted, I double checked the branch name "1d_scanner_optimize." Here are two cases. First, ni_scanner, with a full list of AOs in config file (as default). Second, ni_scanner, without unavailable AOs (and z axis) in config file. Thanks.

1. For ni_scanner, with a full list of AOs ``` Invalid analog source channels encountered. Following sources will be ignored: ao2, ao3 Valid analog input channels are: ai0, ai1, ai2, ai3, ai4, ai5, ai6, ai7, ai8, ai9, ai10, ai11, ai12, ai13, ai14, ai15 Exception during activation: Traceback (most recent call last): File "...\lib\site-packages\qudi\core\module.py", line 301, in __activation_callback self.on_activate() File "...\qudi-iqo-modules\src\qudi\hardware\ni_x_series\ni_x_series_finite_sampling_io.py", line 246, in on_activate raise ValueError( ValueError: The channels "ao2, ao3", specified in the config, were not recognized. Traceback (most recent call last): File "...\lib\site-packages\qudi\core\modulemanager.py", line 201, in activate_module self._modules[module_name].activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() [Previous line repeated 1 more time] File "...\lib\site-packages\qudi\core\modulemanager.py", line 543, in activate raise RuntimeError(f'Failed to activate {self.module_base} module "{self.name}"!') RuntimeError: Failed to activate hardware module "ni_io"! ```
2. For ni_scanner, without unavailable AOs (and z axis) ``` Exception during activation: Traceback (most recent call last): File "...\lib\site-packages\qudi\core\module.py", line 301, in __activation_callback self.on_activate() File "...\qudi-iqo-modules\src\qudi\logic\scanning_probe_logic.py", line 85, in on_activate constr = self.scanner_constraints File "...\qudi-iqo-modules\src\qudi\logic\scanning_probe_logic.py", line 152, in scanner_constraints return self._scanner().get_constraints() File "...\lib\site-packages\qudi\util\overload.py", line 144, in __getattribute__ attr = getattr(obj, name) AttributeError: 'NiScanningProbeInterfuse' object has no attribute 'get_constraints'. Did you mean: '_constraints'? Traceback (most recent call last): File "...\lib\site-packages\qudi\core\modulemanager.py", line 201, in activate_module self._modules[module_name].activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 543, in activate raise RuntimeError(f'Failed to activate {self.module_base} module "{self.name}"!') RuntimeError: Failed to activate logic module "scanning_probe_logic"! ```
TobiasSpohn commented 3 weeks ago

Regarding point 2)

Are you sure that you are running an unmodified scanning_probe_logic.py file as it is in branch 1d_scanner_optimize? Because in the ScanningProbeLogic.scanner_constraints there is no method get_constraints from the scanner called, only the exisiting constraints property, as you can see from the code of the link above. Looking at the repository at an earlier stage the get_constraints method is called. Try using the latest version of the file.

syim70 commented 2 weeks ago

Dear TobiasSpohn, Thank you for your note, and sorry for the confusing error report. I found I did not correctly pull the branch (I am not familiar with git). Here are the errors I encountered.

1. For ni_scanner, with a full list of AOs ``` Invalid analog source channels encountered. Following sources will be ignored: ao2, ao3 Valid analog input channels are: ai0, ai1, ai2, ai3, ai4, ai5, ai6, ai7, ai8, ai9, ai10, ai11, ai12, ai13, ai14, ai15 Exception during activation: Traceback (most recent call last): File "...\lib\site-packages\qudi\core\module.py", line 301, in __activation_callback self.on_activate() File "...\qudi-iqo-modules\src\qudi\hardware\ni_x_series\ni_x_series_finite_sampling_io.py", line 246, in on_activate raise ValueError( ValueError: The channels "ao3, ao2", specified in the config, were not recognized. Traceback (most recent call last): File "...\lib\site-packages\qudi\core\modulemanager.py", line 201, in activate_module self._modules[module_name].activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 502, in activate module.activate() [Previous line repeated 1 more time] File "...\lib\site-packages\qudi\core\modulemanager.py", line 543, in activate raise RuntimeError(f'Failed to activate {self.module_base} module "{self.name}"!') RuntimeError: Failed to activate hardware module "ni_io"! ```
2. For ni_scanner, without unavailable AOs (and z axis) ``` Scan settings in Status Variable empty or invalid, using defaults. Traceback (most recent call last): File "...\qudi-iqo-modules\src\qudi\logic\scanning_optimize_logic.py", line 93, in on_activate self._check_scan_settings() File "...\qudi-iqo-modules\src\qudi\logic\scanning_optimize_logic.py", line 377, in _check_scan_settings ax.position.check(self.scan_range[name]) KeyError: 'x' Exception during activation: Traceback (most recent call last): File "...\lib\site-packages\qudi\core\module.py", line 301, in __activation_callback self.on_activate() File "...\qudi-iqo-modules\src\qudi\gui\scanning\scannergui.py", line 186, in on_activate self._init_static_dockwidgets() File "...\qudi-iqo-modules\src\qudi\gui\scanning\scannergui.py", line 423, in _init_static_dockwidgets self.optimizer_dockwidget = OptimizerDockWidget(axes=self._scanning_logic().scanner_axes, File "...\qudi-iqo-modules\src\qudi\gui\scanning\optimizer_dockwidget.py", line 60, in __init__ for i_col, n_dim in enumerate(plot_dims): TypeError: 'ConfigOption' object is not iterable Traceback (most recent call last): File "...\lib\site-packages\qudi\core\modulemanager.py", line 201, in activate_module self._modules[module_name].activate() File "...\lib\site-packages\qudi\core\modulemanager.py", line 543, in activate raise RuntimeError(f'Failed to activate {self.module_base} module "{self.name}"!') RuntimeError: Failed to activate gui module "scanner_gui"! ```
timoML commented 2 weeks ago

Can you poste the relevant parts (the modules mentioned here) of your config file for both cases?

TobiasSpohn commented 2 weeks ago

Hi @syim70,

For me the first error seems like you are trying to configure input channels as outputs. Try looking into the config to see if you configure the right channels for inputs and outputs, as I don't know, whether you could use output channels (ao) as input channels (ai).

The second error also seems like you are running an outdated version of the gui or logic files. The error TypeError: 'ConfigOption' object is not iterable occurs when a ConfigOption fails to correctly initialize as normally it should be converted to another type upon initialization, in this case it should be a Tuple. We removed the plot_dims ConfigOption in favor of a StatusVariable that can be set e.g. in the GUI. So the plot_dims variable should no longer be a ConfigOption in the first place. Try updating the files for the entire toolchain. The KeyError: 'x' is just a warning that occurs on first loading of the toolchain when defaults are initialized and once you successfully load the toolchain it should no longer be present.

syim70 commented 2 weeks ago

Hi, timoML,

I post my config file for the both cases. Thanks.

1. For ni_scanner, with a full list of AOs ``` gui: scanner_gui: module.Class: 'scanning.scannergui.ScannerGui' options: image_axes_padding: 0.02 default_position_unit_prefix: null # optional, use unit prefix characters, e.g. 'u' or 'n' optimizer_plot_dimensions: [2] # xy only (z axis off) connect: scanning_logic: scanning_probe_logic data_logic: scanning_data_logic optimize_logic: scanning_optimize_logic logic: scanning_probe_logic: module.Class: 'scanning_probe_logic.ScanningProbeLogic' options: max_history_length: 20 max_scan_update_interval: 2 position_update_interval: 1 connect: #scanner: scanner_dummy scanner: ni_scanner scanning_data_logic: module.Class: 'scanning_data_logic.ScanningDataLogic' options: max_history_length: 20 connect: scan_logic: scanning_probe_logic scanning_optimize_logic: module.Class: 'scanning_optimize_logic.ScanningOptimizeLogic' connect: scan_logic: scanning_probe_logic hardware: ni_scanner: module.Class: 'interfuse.ni_scanning_probe_interfuse.NiScanningProbeInterfuse' # to use without tilt correction # module.Class: 'interfuse.ni_scanning_probe_interfuse.NiScanningProbeInterfuseBare' connect: scan_hardware: 'ni_io' analog_output: 'ni_ao' options: ni_channel_mapping: x: 'ao0' y: 'ao1' z: 'ao2' APD1: 'PFI8' APD2: 'PFI9' AI0: 'ai0' position_ranges: # in m x: [-100e-6, 100e-6] y: [-100e-6, 100e-6] z: [-100e-6, 100e-6] frequency_ranges: #Aka values written/retrieved per second; Check with connected HW for sensible constraints. x: [1, 5000] y: [1, 5000] z: [1, 1000] resolution_ranges: x: [1, 10000] y: [1, 10000] z: [2, 1000] input_channel_units: APD1: 'c/s' APD2: 'c/s' AI0: 'V' backwards_line_resolution: 50 # optional move_velocity: 400e-6 #m/s; This speed is used for scanner movements and avoids jumps from position to position. ni_io: module.Class: 'ni_x_series.ni_x_series_finite_sampling_io.NIXSeriesFiniteSamplingIO' options: device_name: 'Dev1' input_channel_units: PFI8: 'c/s' PFI9: 'c/s' ai0: 'V' ai1: 'V' output_channel_units: # Specify used output channels 'ao0': 'V' 'ao1': 'V' 'ao2': 'V' 'ao3': 'V' adc_voltage_ranges: ai0: [-10, 10] # optional ai1: [-10, 10] # optional output_voltage_ranges: ao0: [-10, 10] ao1: [-10, 10] ao2: [-10, 10] ao3: [-10.0, 10.0] frame_size_limits: [1, 1e9] # optional #TODO actual HW constraint? default_output_mode: 'JUMP_LIST' # optional, must be name of SamplingOutputMode read_write_timeout: 10 # optional sample_clock_output: '/Dev1/PFI11' # optional: routing of sample clock to a physical connection ni_ao: module.Class: 'ni_x_series.ni_x_series_analog_output.NIXSeriesAnalogOutput' options: device_name: 'Dev1' channels: ao0: limits: [-10.0, 10.0] keep_value: True ao1: limits: [-10.0, 10.0] keep_value: True ao2: limits: [-10.0, 10.0] keep_value: True ```
2. For ni_scanner, without unavailable AOs (and z axis) ``` gui: scanner_gui: module.Class: 'scanning.scannergui.ScannerGui' options: image_axes_padding: 0.02 default_position_unit_prefix: null # optional, use unit prefix characters, e.g. 'u' or 'n' optimizer_plot_dimensions: [2] # xy only (z axis off) connect: scanning_logic: scanning_probe_logic data_logic: scanning_data_logic optimize_logic: scanning_optimize_logic logic: scanning_probe_logic: module.Class: 'scanning_probe_logic.ScanningProbeLogic' options: max_history_length: 20 max_scan_update_interval: 2 position_update_interval: 1 connect: #scanner: scanner_dummy scanner: ni_scanner scanning_data_logic: module.Class: 'scanning_data_logic.ScanningDataLogic' options: max_history_length: 20 connect: scan_logic: scanning_probe_logic scanning_optimize_logic: module.Class: 'scanning_optimize_logic.ScanningOptimizeLogic' connect: scan_logic: scanning_probe_logic hardware: ni_scanner: module.Class: 'interfuse.ni_scanning_probe_interfuse.NiScanningProbeInterfuse' # to use without tilt correction # module.Class: 'interfuse.ni_scanning_probe_interfuse.NiScanningProbeInterfuseBare' connect: scan_hardware: 'ni_io' analog_output: 'ni_ao' options: ni_channel_mapping: x: 'ao0' y: 'ao1' # z: 'ao2' APD1: 'PFI8' APD2: 'PFI9' AI0: 'ai0' position_ranges: # in m x: [-100e-6, 100e-6] y: [-100e-6, 100e-6] # z: [-100e-6, 100e-6] frequency_ranges: #Aka values written/retrieved per second; Check with connected HW for sensible constraints. x: [1, 5000] y: [1, 5000] # z: [1, 1000] resolution_ranges: x: [1, 10000] y: [1, 10000] # z: [2, 1000] input_channel_units: APD1: 'c/s' APD2: 'c/s' AI0: 'V' backwards_line_resolution: 50 # optional move_velocity: 400e-6 #m/s; This speed is used for scanner movements and avoids jumps from position to position. ni_io: module.Class: 'ni_x_series.ni_x_series_finite_sampling_io.NIXSeriesFiniteSamplingIO' options: device_name: 'Dev1' input_channel_units: PFI8: 'c/s' PFI9: 'c/s' ai0: 'V' ai1: 'V' output_channel_units: # Specify used output channels 'ao0': 'V' 'ao1': 'V' # 'ao2': 'V' # 'ao3': 'V' adc_voltage_ranges: ai0: [-10, 10] # optional ai1: [-10, 10] # optional output_voltage_ranges: ao0: [-10, 10] ao1: [-10, 10] # ao2: [-10, 10] # ao3: [-10.0, 10.0] frame_size_limits: [1, 1e9] # optional #TODO actual HW constraint? default_output_mode: 'JUMP_LIST' # optional, must be name of SamplingOutputMode read_write_timeout: 10 # optional sample_clock_output: '/Dev1/PFI11' # optional: routing of sample clock to a physical connection ni_ao: module.Class: 'ni_x_series.ni_x_series_analog_output.NIXSeriesAnalogOutput' options: device_name: 'Dev1' channels: ao0: limits: [-10.0, 10.0] keep_value: True ao1: limits: [-10.0, 10.0] keep_value: True # ao2: # limits: [-10.0, 10.0] # keep_value: True ```
syim70 commented 2 weeks ago

Hi @syim70,

For me the first error seems like you are trying to configure input channels as outputs. Try looking into the config to see if you configure the right channels for inputs and outputs, as I don't know, whether you could use output channels (ao) as input channels (ai).

The second error also seems like you are running an outdated version of the gui or logic files. The error TypeError: 'ConfigOption' object is not iterable occurs when a ConfigOption fails to correctly initialize as normally it should be converted to another type upon initialization, in this case it should be a Tuple. We removed the plot_dims ConfigOption in favor of a StatusVariable that can be set e.g. in the GUI. So the plot_dims variable should no longer be a ConfigOption in the first place. Try updating the files for the entire toolchain. The KeyError: 'x' is just a warning that occurs on first loading of the toolchain when defaults are initialized and once you successfully load the toolchain it should no longer be present.

Hi, TobiasSpohn,

First, I was not trying to configure a something special, but just used the default config file as it is, except the dimensions as [2]. So, I don't agree with your guess that the first error might come from the confusing the input and output channels.

I am not a code developer, so I hope using a stabilized code (the latest one, but not a pre-release). I am using a qudi-core (v.1.5.1) and qudi-iqo-modules (v.0.5.1). Last time, I found my misunderstanding of git, but now I believe I correctly pulled the "1d_scanner_optimze" branch. What you mean the "outdated version" is v.0.5.1? Should I pull some relevant branches altogether?

Thank you so much for your efforts.

TobiasSpohn commented 4 days ago

Hi,

For 1: In your config I don't spot any obvious errors, it seems fine. I personally use a very similar configuration. However, the error you posted above seems to me that you are trying to configure output channels where it should be input channels. Maybe your card does not support that many input or output channels? Because this error message suggests that you are trying to configure invalid channels.

Invalid analog source channels encountered. Following sources will be ignored: ao2, ao3 Valid analog input channels are: ai0, ai1, ai2, ai3, ai4, ai5, ai6, ai7, ai8, ai9, ai10, ai11, ai12, ai13, ai14, ai15

It even lists the available channels below, you will have to try changing to the correct channels.

For 2.: If you are checking out a development branch, you are no longer working with a release (e.g. v0.5.1), but the development version of qudi. The main branch should still be stable, although some minor bugs might occur, which are mostly hotfixed pretty quickly. We are currently working on merging the 1d_scanner_optimize into main branch, however this is still a pre-release. A new release with these new features appended to, will still take some time after that. Just from your error messages you posted above you have some error occuring: for i_col, n_dim in enumerate(plot_dims): TypeError: 'ConfigOption' object is not iterable. This error occurs when a ConfigOption (the options you specify in your config file) fails to initialize. However, with the current state of 1d_scanner_optimize there is no ConfigOption plot_dims, as we removed it in favor of a graphical and cli way to change the plot_dims during runtime. Looking at the branch in an earlier state (before we made the fixes) one can see that the ConfigOption is present in the code. This means you have not updated your (whole) file with the latest changes of 1d_scanner_optimize. Please make sure, especially when using a graphical program, e.g. the git utility in Pycharm, that you actually update everything from the remote branch and not keep some local changes.