Flame-S Edge Trigger Mode and Timing

[waldowda]

spectrometer and system information

• model: Flame-S supposed to be the same as USB-2000PLUS I believe
• operating system: MacOS 15.5.5 or Win10 current
• python version: 3.7.7 (via Anaconda) or 3.8.x
• python-seabreeze version: v1.1.0 I believe
• installed-via: conda and python for anaconda

current problem

This issue is branched from a previous issue regarding the Flame-S --> "Flame-S spectrometer is seen but doesn't report data #92".

(Andreas: Sorry this is long but hopefully understandable and helpful. Dean )

First Trigger / Timing Issue

I suspect the settings for triggering the HR2000+, USB2000+, and Flame-S are missing edge triggering unless the trigger numbers one specifies are not the same as the manuals.

I heard back from OI regarding discrepancies in the manuals and per your suggestion I am starting a new issue.

Here is what tech support said which is consistent with page 34 above from the USB2000+ manual and from the Flame for the Flame-S spectrometer:

The Flame-S has 4 trigger modes:
    • On Demand (normal mode): mode 0
    • Edge: mode 4
    • Level: mode 2
    • Synchronous: mode 3

Note that they leave out '1' which is described as a software trigger...

and from the part of the Flame manual that is consistent with the note from tech support (though in other parts of the manual it appears to have contradictory settings). I suspect this issue has to do with the differences between the Flame-S and Flame-T models where the latter one seems have the other set of trigger values seen in the manual.

HR2000+, USB2000+ and Flame-S Set Trigger Mode
Data Value = 0 -> Normal (Free running) Mode
Data Value = 1 -> Software Trigger Mode
Data Value = 2  ->  External Hardware Level Trigger Mode 
Data Value = 3 -> External Synchronization Trigger Mode 
Data Value = 4 -> External Hardware Edge Trigger Mode

From my testing of both cseabreeze and py-seabreeze...

import seabreeze
seabreeze.use('cseabreeze')

#seabreeze.use('pyseabreeze')

from seabreeze.spectrometers import list_devices, Spectrometer

spec = Spectrometer.from_serial_number("FLMS16723")
spec.trigger_mode(0)

So, if the data value for the trigger info: "T(word)" in py/c-seabreeze goes from 0 to 3, then I suspect it will not be possible to setup edge trigger mode which is '4'. However, if there is an internal translation from 0...3 to 0, 4, 2, 3 then perhaps but it is not clear to me if that is the case.

I was able to add '4' to the NI Labview trigger subVI and was able to trigger. I can't figure out if I can modify the py-seabreeze code to add trigger mode 4 or even if that would be the correct thing to do.

I have found the following in spectrometers.py but I have not been able to go past this to see where trigger mode gets set.

 def trigger_mode(self, mode):
        """set the trigger mode of the device

        Parameters
        ----------
        mode : `int`
            refer to your spectrometer's datasheet to determine the correct
            value for the trigger mode you want to use.
        """
        self._dev.f.spectrometer.set_trigger_mode(mode)

Second Trigger / Timing Issue

Second regarding timing of acquiring data. Previously, I measured the average time to acquire a spectrum as a function of integration time and at about 1600 microseconds there is a jump down in acquisition time. Even though I would like that to be accurate I suspect it is an issue in that py-seabreeze might be reporting the spectrum before it is read out of the CCD. Here is what I found as previously reported. In this case, I am triggering in trigger mode 0 (free running). This was acquired on a Mac but it is very similar on a win10 box.

And I suspect there is some sort of process prioritization that may be computer dependent that adds an approximately constant call time to the loop so the time per scan goes down... I think the main question is why the change in behavior at 1600 µs for integration time?

I have seen this from both win10 and macOS.

The External triggering options firmware3.0 and above PDF file, it has the following timing diagram which I am not sure it the timing would apply to a free running spectrometer but it might providing some insight:

The reason I am doing this is to use edge triggering to sync timing with a Gamry potentiostat which I can set to have an output pulse at each data point and then I turn off edge triggering and acquire 'X' spectra to average then turn on edge triggering again and wait for the next pulse.

I am wondering if the spectrometer will return values for the spectrum even before a new one is acquired.

steps to reproduce

Execute the code below to set edge triggering.

minimal code example and error (very helpful if available)

import seabreeze
seabreeze.use('cseabreeze')

#seabreeze.use('pyseabreeze')

from seabreeze.spectrometers import list_devices, Spectrometer

spec = Spectrometer.from_serial_number("FLMS16723")

#for edge trigger per information from the manual.
spec.trigger_mode(4)

and in devices.py

class TriggerMode(enum.IntEnum):
    """internal trigger modes enum"""

    NORMAL = 0x00
    SOFTWARE = 0x01
    LEVEL = 0x01
    SYNCHRONIZATION = 0x02
    HARDWARE = 0x03
    EDGE = 0x03
    SINGLE_SHOT = 0x04
    SELF_NORMAL = 0x80
    SELF_SOFTWARE = 0x81
    SELF_SYNCHRONIZATION = 0x82
    SELF_HARDWARE = 0x83
    DISABLED = 0xFF
    OBP_NORMAL = 0x00
    OBP_EXTERNAL = 0x01
    OBP_INTERNAL = 0x02

    @classmethod
    def supported(cls, *mode_strings):
        return set(getattr(cls, mode_string) for mode_string in mode_strings)

Hum? Should EDGE be 0x04 like SINGLE_SHOT?

Maybe this would fix things? I'll try it.

# SPECTROMETER DEFINITIONS
# ========================
#
class USB2000PLUS(SeaBreezeDevice):

    model_name = "USB2000PLUS"

    # communication config
    transport = (USBTransport,)
    usb_product_id = 0x101E
    usb_endpoint_map = EndPointMap(
        ep_out=0x01, lowspeed_in=0x81, highspeed_in=0x82, highspeed_in2=0x86
    )
    usb_protocol = OOIProtocol

    # spectrometer config
    dark_pixel_indices = DarkPixelIndices.from_ranges((6, 21))  # as in seabreeze-3.0.9
    integration_time_min = 1000
    integration_time_max = 655350000
    integration_time_base = 1
    spectrum_num_pixel = 2048
    spectrum_raw_length = (2048 * 2) + 1
    spectrum_max_value = 65535
    #"NORMAL", "SOFTWARE", "SYNCHRONIZATION", "HARDWARE"
    trigger_modes = TriggerMode.supported(
        "NORMAL", "SOFTWARE", "SYNCHRONIZATION", "HARDWARE", "SINGLE_SHOT"
    )

    # features
    feature_classes = (
        sbf.eeprom.SeaBreezeEEPromFeatureOOI,
        sbf.spectrometer.SeaBreezeSpectrometerFeatureUSB2000PLUS,
        sbf.continuousstrobe.SeaBreezeContinuousStrobeFeatureOOI,
        sbf.rawusb.SeaBreezeRawUSBBusAccessFeature,
    )

I tried this but it sort of seems to work in that in pyseabreeze it doesn't error for a mode of 4 but there are other issues.

#data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
data = spec.intensities()

The spectrometer can correct for dark counts and nonlinearity but when I set those to true it errors as follows. This may be independent of the trigger mode.

Here is what happens with some example code without changing triggering:

import numpy
import time
import matplotlib.pyplot as plt

# explicitly request pyseabreeze
import seabreeze
#seabreeze.use('cseabreeze')

seabreeze.use('pyseabreeze')

from seabreeze.spectrometers import list_devices, Spectrometer

devices = list_devices()

print (devices)

spec = Spectrometer.from_serial_number("FLMS16723")

print ("Serial Number: ", spec.serial_number)
print ("Max Intensity: ", spec.max_intensity)
print ("Min. Int. Time: ",spec.minimum_integration_time_micros)
print ("Stray Light Coef",spec.stray_light_coeffs)
print ("Trigger Mode: ",spec.trigger_mode)

spec.integration_time_micros(1000)
#spec.boxcar_width(4)

wavelengths = spec.wavelengths()
print ("Wavelengths: ", wavelengths)

#data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
data = spec.intensities()

print ("Dim: ", data.ndim)
print ("Shape: ", data.shape)
print ("size: ", data.size)
data[0]
data

print ("Intensities: ", data)

plt.plot(wavelengths,data)
plt.show()

start_time = time.time_ns()
print ("Start time: ", start_time)
#data1 = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
data1 = spec.intensities()
stop_time = time.time_ns()
print ("Stop time: ", stop_time)
total_time = (stop_time - start_time)/1000
print ("Total time (µs): ", total_time)

print ("Intensities: ", data1)

exception but it runs:

Exception ignored in: <function _AutoFinalizedObjectBase.__del__ at 0x0000022655576820>
Traceback (most recent call last):
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 84, in __del__
    self.finalize()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 144, in finalize
    self._finalizer()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\weakref.py", line 566, in __call__
    return info.func(*info.args, **(info.kwargs or {}))
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 104, in _do_finalize_object_ref
    obj._do_finalize_object()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 71, in _do_finalize_object
    self._finalize_object()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\backend\libusb1.py", line 604, in _finalize_object
    _lib.libusb_unref_device(self.devid)
OSError: exception: access violation writing 0x0000000000000024

If I change to:

data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
#data = spec.intensities()

Then I get the following errors even though the spectrometer supports both modes and it works in cseabreeze as far as I can tell.

[<SeaBreezeDevice USB2000PLUS:FLMS16723>]
Serial Number:  FLMS16723
Max Intensity:  65535.0
Min. Int. Time:  1000
Stray Light Coef <bound method DeprecatedSpectrometerMixin.stray_light_coeffs of <Spectrometer USB2000PLUS:FLMS16723>>
Trigger Mode:  <bound method Spectrometer.trigger_mode of <Spectrometer USB2000PLUS:FLMS16723>>
Wavelengths:  [ 339.8952      340.27820458  340.66116785 ... 1026.47833653 1026.76169767
 1027.04500266]
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-195d4932b562> in <module>
     30 print ("Wavelengths: ", wavelengths)
     31 
---> 32 data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
     33 #data = spec.intensities()
     34 

~\.conda\envs\SpecEchem Environment\lib\site-packages\seabreeze\spectrometers.py in intensities(self, correct_dark_counts, correct_nonlinearity)
    177             measured intensities in (a.u.)
    178         """
--> 179         if correct_dark_counts and not self._dp:
    180             raise self._backend.SeaBreezeError(
    181                 "This device does not support dark count correction."

ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

But... the following works apparently:

spec.trigger_mode(4)

It doesn't error. I will add more if I can get it to trigger from the potentiostat but that is all I have time for now.

[ap--]

Hi Dean,

Thank you for the really detailed error description! 🥇 This makes solving issues a lot easier. Also with the newer version of seabreeze out, let's start debugging your issue.

First: the way you added the new TriggerMode is correct! 😃👍 Basically pyseabreeze just blocks using unsupported triggermodes from getting send to the spectrometer and when you added SINGLE_SHOT to the TriggerModes.supported() call you allowed it to be passed through.

Second: the darkcount error you get is definitely a bug. And I thought I fixed this a long time ago already... Can you show the output of:

import seabreeze
print(seabreeze.__version__)

Let's solve the darkcount issue first, and then move towards the trigger issue.

Also, just to let you know: I have a work in progress branch where I implement that the Flame-S will be recognized correctly and will push that soon. But time is currently a scarce commodity so it's hard for me to predict when I can continue to work on it. Let's try to get out the dark count issue because that should make everything you need for now. Then we'll add the trigger mode to a new version of seabreeze and then we'll investigate the constant time offset issue 😅

Cheers, Andreas 😃

[waldowda]

Hi Andreas, I just saw your message. I think you are correct that if we can get the Dark to work then I can get the trigger '4' single shot to work and can actually start putting the potentiostat with the spectrometer. I tested some OI py code but it is not ready for this application yet. Did I understand that there is a new py-seabreeze version? Well, I'll do the test first.

import numpy
import time
import matplotlib.pyplot as plt

# explicitly request pyseabreeze
import seabreeze
#seabreeze.use('cseabreeze')
seabreeze.use('pyseabreeze')

print(seabreeze.__version__)

from seabreeze.spectrometers import list_devices, Spectrometer

devices = list_devices()

print (devices)

Output:

1.1.0
[<SeaBreezeDevice USB2000PLUS:FLMS16723>]

Version: 1.1.0

Dean

[ap--]

Hi Dean,

~1.1.0 should already have the bugfix. I guess I made some mistake there.~ (I was wrong. The dark pixel fix landed in 1.2.0.)

And yes, the newest version is 1.2.0 and I released it yesterday. It fixed a few small issues with test and usb-transport handling. But should not change anything for you.

I'll try to reproduce the darkcount error on my machine tomorrow. Will have to sign off for today!

Have a nice day, Andreas 😃

[waldowda]

OK... I'll try the py vs c - seabreeze test again on both my surface pro 7 and MacBook pro... maybe it is an OS issue but doubt it and update if I find anything useful. I have many zoom meetings today so it might take a bit. Regards, Dean

Update 1:

I have gotten the py-seabreeze code to work on an environment on my mac but not on the PC. I can't tell if I did something different on the PC. Also, the version that is working doesn't have the modification for SINGLE_SHOT. Not sure why now it is working on one and not the other. Could there be a difference in a class it calls?

Still on the mac, I think I was fooled. I tried to restart using pyseabreeze after running using cseabreeze and it appeared to work but it still was hooked onto cseabreeze. I am a bit puzzled as now something is not allowing the backend to load.

import numpy
import time
import matplotlib.pyplot as plt

# explicitly request pyseabreeze
import seabreeze
#seabreeze.use('cseabreeze')
seabreeze.use('pyseabreeze')

print(seabreeze.__version__)

from seabreeze.spectrometers import list_devices, Spectrometer

devices = list_devices()

print (devices)

spec = Spectrometer.from_serial_number("FLMS16723")

print ("Serial Number: ", spec.serial_number)
print ("Max Intensity: ", spec.max_intensity)
print ("Min. Int. Time: ",spec.minimum_integration_time_micros)
print ("Stray Light Coef",spec.stray_light_coeffs)
#print ("Trigger Mode: ",spec.trigger_mode)

seabreeze can't load 'pyseabreeze' backend - error: 'ModuleNotFoundError("No module named 'usb'")'
Traceback (most recent call last):
  File "/Users/waldow/opt/anaconda3/envs/specechem/lib/python3.7/site-packages/seabreeze/backends.py", line 15, in _use_backend
    import seabreeze.pyseabreeze as sbb
  File "/Users/waldow/opt/anaconda3/envs/specechem/lib/python3.7/site-packages/seabreeze/pyseabreeze/__init__.py", line 4, in <module>
    from seabreeze.pyseabreeze.api import SeaBreezeAPI
  File "/Users/waldow/opt/anaconda3/envs/specechem/lib/python3.7/site-packages/seabreeze/pyseabreeze/api.py", line 11, in <module>
    import usb.core
ModuleNotFoundError: No module named 'usb'
1.1.0
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-fa7106b63db5> in <module>
     10 print(seabreeze.__version__)
     11 
---> 12 from seabreeze.spectrometers import list_devices, Spectrometer
     13 
     14 devices = list_devices()

~/opt/anaconda3/envs/specechem/lib/python3.7/site-packages/seabreeze/spectrometers.py in <module>
     13 
     14 # get the backend and add some functions/classes to this module
---> 15 _lib = seabreeze.backends.get_backend()
     16 
     17 SeaBreezeError = _lib.SeaBreezeError

~/opt/anaconda3/envs/specechem/lib/python3.7/site-packages/seabreeze/backends.py in get_backend()
     93 
     94     if backend is None:
---> 95         raise ImportError("Could not import backend. Requested: {}".format(requested))
     96 
     97     return backend

ImportError: Could not import backend. Requested: pyseabreeze

On the PC side, I maybe have more info. I get warnings before the logic error:

Exception ignored in: <function _AutoFinalizedObjectBase.__del__ at 0x000001C24EBF68B0>
Traceback (most recent call last):
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 84, in __del__
    self.finalize()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 144, in finalize
    self._finalizer()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\weakref.py", line 566, in __call__
    return info.func(*info.args, **(info.kwargs or {}))
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 104, in _do_finalize_object_ref
    obj._do_finalize_object()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\_objfinalizer.py", line 71, in _do_finalize_object
    self._finalize_object()
  File "C:\Users\waldowda\.conda\envs\SpecEchem Environment\lib\site-packages\usb\backend\libusb1.py", line 604, in _finalize_object
    _lib.libusb_unref_device(self.devid)
OSError: exception: access violation writing 0x0000000000000024
1.1.0
[<SeaBreezeDevice USB2000PLUS:FLMS16723>]

I'll look again tomorrow if I can get time. Maybe I should reinstall anaconda again anew?

[waldowda]

I wanted to setup another test on the surface pro 7 from a new environment. I made a new environment with python 3.8 and did a pip install seabreeze (1.2.0) then realized that it didn't install py-seabreeze so then issued "pip install seabreeze[pyseabreeze]". Since I had already installed drivers before via 1.1.0, I didn't worry about the following error for seabreeze_os_setup. Maybe this is a problem?

Install windows drivers? [y/n] y
Downloading windows drivers from github
Error when installing drivers
Press [enter] to close.

To test, I using the following code first and in creating a spectrometer it erred in a manner I have not seen. An eeprom error.

import numpy
import time
import matplotlib.pyplot as plt

# explicitly request pyseabreeze
import seabreeze
#seabreeze.use('cseabreeze')

seabreeze.use('pyseabreeze')

print (seabreeze.__version__)

from seabreeze.spectrometers import list_devices, Spectrometer

devices = list_devices()

print (devices)

and got the following back:

1.2.0
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-3-6308e1042135> in <module>
     11 print (seabreeze.__version__)
     12 
---> 13 from seabreeze.spectrometers import list_devices, Spectrometer
     14 
     15 devices = list_devices()

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\spectrometers.py in <module>
     13 
     14 # get the backend and add some functions/classes to this module
---> 15 _lib = seabreeze.backends.get_backend()
     16 
     17 SeaBreezeError = _lib.SeaBreezeError

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\backends.py in get_backend()
     76     backends = _SeaBreezeConfig["available_backends"]
     77 
---> 78     backend = _use_backend(requested)  # trying to import requested backend
     79     if backend is None and fallback:
     80 

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\backends.py in _use_backend(name)
     13             import seabreeze.cseabreeze as sbb
     14         elif name == "pyseabreeze":
---> 15             import seabreeze.pyseabreeze as sbb
     16         else:
     17             raise ValueError("unknown backend '{}'".format(name))

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\pyseabreeze\__init__.py in <module>
      2 
      3 """
----> 4 from seabreeze.pyseabreeze.api import SeaBreezeAPI
      5 from seabreeze.pyseabreeze.devices import SeaBreezeDevice
      6 from seabreeze.pyseabreeze.exceptions import SeaBreezeError, SeaBreezeNumFeaturesError

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\pyseabreeze\api.py in <module>
     10 import weakref
     11 
---> 12 from seabreeze.pyseabreeze.devices import SeaBreezeDevice, _model_class_registry
     13 from seabreeze.pyseabreeze.transport import (
     14     USBTransport,

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\pyseabreeze\devices.py in <module>
    429 # ========================
    430 #
--> 431 class USB2000PLUS(SeaBreezeDevice):
    432 
    433     model_name = "USB2000PLUS"

~\.conda\envs\pyseabreeze\lib\site-packages\seabreeze\pyseabreeze\devices.py in USB2000PLUS()
    455     # features
    456     feature_classes = (
--> 457         sbf.eeprom.SeaBreezeEEPromFeatureOOI,
    458         sbf.spectrometer.SeaBreezeSpectrometerFeatureUSB2000PLUS,
    459         sbf.continuousstrobe.SeaBreezeContinuousStrobeFeatureOOI,

AttributeError: module 'seabreeze.pyseabreeze.features' has no attribute 'eeprom'

I doubt this is that helpful but thought I would pass it along. Maybe it is related or may be new per 1.2.0. BTW, cseabreeze continues to work as in the past. I just can't change the triggering options. I'll update if I learn more.

[ap--]

Hi Dean,

So the seabreeze_os_setup windows error is something i've had troubles to reproduce lately. But I've definitely seen it too. I created a new issue #99 for that.

That the eeprom feature is missing is very strange. I'll put that on my list for trying to reproduce.

Cheers, Andreas 😃

[waldowda]

I am beginning to wonder if some of these errors might be connected to a particular anaconda environment or win10 / MacOS permissions. I am going to try two things: 1) not use anaconda on my win10 box but the chocolaty procedure (though I like anaconda's flexibility) and 2) on my MacOS box, try to install in a fresh environment. It sure seems like we are close to have the Flame-S working nicely. I may end up finishing my Labview version to get things running since my teaching schedule will get heavy shortly. BTW: I have not run that test you asked about for the development version. I was not confident I was able to download and install the dev version properly. Regards, Dean

[ap--]

Okay, small update:

• [x] The dark pixel issue was still present in 1.1.0 and is fixed in 1.2.0. I was wrong about that.
• [ ] I'll have a look at the seabreeze_os_setup issue next
• [ ] Then we'll investigate the TriggerMode issue

Regarding anaconda: It's totally fine if you keep on using anaconda. For now make sure that you create a conda environment with python=3.8 that will rule out a few suspicions I have regarding failing SSL certs for seabreeze_os_setup

[waldowda]

OK. If I understand your first point... the dark pixel issue is the reason I can't set True to Dark and nonlinearity correction in the get spectrum call and it is currently not fixed in version 1.2.0? Second, I'll transition to anaconda environments with python 3.8. Thanks! I think if I can get the dark part fixed I can patch the '4' setting temporarily but having py-seabreeze recognize Flame-S and have the trigger settings match would be great.

Update 20200813: FYI: I setup a new anaconda 3.8 environment on my MacOS 10.15.6. When I issued the install command for pyseabreeze only pip didn't find anything but seabreeze alone worked OK.

(pyseabreeze) waldow@x86_64-apple-darwin13 ~ % pip install seabreeze[pyseabreeze] --no-use-pep517 --no-build-isolation --install-option="--without-cseabreeze"
zsh: no matches found: seabreeze[pyseabreeze]

Though when I issued just seabreeze it seemed good.

(pyseabreeze) waldow@x86_64-apple-darwin13 ~ % pip install seabreeze                                                                                           
Collecting seabreeze
  Downloading seabreeze-1.2.0-cp38-cp38-macosx_10_9_x86_64.whl (898 kB)
     |████████████████████████████████| 898 kB 6.7 MB/s 
Collecting future
  Using cached future-0.18.2.tar.gz (829 kB)
Requirement already satisfied: numpy; python_version >= "3.7" in ./opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages (from seabreeze) (1.19.1)
Building wheels for collected packages: future
  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=0980e2a8ec4114a36a635495cb6ac08c4d7c94b76fba1d02b69238f4012c75a2
  Stored in directory: /Users/waldow/Library/Caches/pip/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built future
Installing collected packages: future, seabreeze
Successfully installed future-0.18.2 seabreeze-1.2.0

Will test spec.intensities(correct_dark_counts=True, correct_nonlinearity=True) when I am back at the spectrometer.

Update 20200813 5pm PST

I tried to run the following code when I got home which is where I am trying to do development on due to COVID.

import numpy
import time
import matplotlib.pyplot as plt

# explicitly request pyseabreeze
import seabreeze
#seabreeze.use('cseabreeze')
seabreeze.use('pyseabreeze')

print(seabreeze.__version__)

from seabreeze.spectrometers import list_devices, Spectrometer

devices = list_devices()

print (devices)

spec = Spectrometer.from_serial_number("FLMS16723")

print ("Serial Number: ", spec.serial_number)
print ("Max Intensity: ", spec.max_intensity)
print ("Min. Int. Time: ",spec.minimum_integration_time_micros)
print ("Stray Light Coef",spec.stray_light_coeffs)
#print ("Trigger Mode: ",spec.trigger_mode)

It is grumpy due to seabreeze backend USB errors:

seabreeze can't load 'pyseabreeze' backend - error: 'ModuleNotFoundError("No module named 'usb'")'
Traceback (most recent call last):
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/backends.py", line 15, in _use_backend
    import seabreeze.pyseabreeze as sbb
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/__init__.py", line 4, in <module>
    from seabreeze.pyseabreeze.api import SeaBreezeAPI
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/api.py", line 12, in <module>
    from seabreeze.pyseabreeze.devices import SeaBreezeDevice, _model_class_registry
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/devices.py", line 11, in <module>
    from seabreeze.pyseabreeze import features as sbf
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/features/__init__.py", line 30, in <module>
    from seabreeze.pyseabreeze.features.rawusb import SeaBreezeRawUSBBusAccessFeature
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/features/rawusb.py", line 3, in <module>
    from seabreeze.pyseabreeze.transport import USBTransport
  File "/Users/waldow/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/transport.py", line 12, in <module>
    import usb.core
ModuleNotFoundError: No module named 'usb'

It does print 1.2.0 for the seabreeze version.

Then errors also when I call from seabreeze.spectrometers import list_devices, Spectrometer due presumably to the usb.core error above.

Again, if I switch to cseabreeze, then usb seems to work again:

1.2.0
[<SeaBreezeDevice USB2000PLUS:FLMS16723>]
Serial Number:  FLMS16723
Max Intensity:  65535.0
Min. Int. Time:  1000
Stray Light Coef <bound method DeprecatedSpectrometerMixin.stray_light_coeffs of <Spectrometer USB2000PLUS:FLMS16723>>

Dark and nonlinear correction work nicely. But, I can't select trigger mode '4' and can't tweak the cseabreeze as I believe it is compiled.

Then, I figured something was missing from the environment. I found pyusb and installed it. Shutown anaconda, and restarted anaconda as well as disconnecting and reconnecting the Flame-S. Does pyseabreeze have a dependency on this and it is not caught in the pip install?

Now it gets through the from seabreeze.spectrometers import list_devices, Spectrometer command portion above.

But, neither dark or nonlinearity correction work but without them I get spectra. Note, I added another test to see if it is only dark but nonlinearity also triggers the error.

SeaBreezeError                            Traceback (most recent call last)
<ipython-input-13-f7b9a39b7dbf> in <module>
      5 print ("Wavelengths: ", wavelengths)
      6 
----> 7 data = spec.intensities(correct_nonlinearity=True)
      8 #data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
      9 #data = spec.intensities()

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/spectrometers.py in intensities(self, correct_dark_counts, correct_nonlinearity)
    183             )
    184         if correct_nonlinearity and not self._nc:
--> 185             raise self._backend.SeaBreezeError(
    186                 "This device does not support nonlinearity correction."
    187             )

SeaBreezeError: This device does not support nonlinearity correction.

Could I have done something wrong in setting up the environment? You suggest that the bug related to this is fixed. Don't mean to disagree. 😄

I'll give it a try on the windows box next.

20200813 later

OK... did a quick test with windows10 on a surface pro 7. I built another python 3.8 environment the same as above. USB was not found. I installed pyusb. It errors in a different way. Rebooted. Tried again and got for the same initial code as above:

1.2.0
---------------------------------------------------------------------------
NoBackendError                            Traceback (most recent call last)
~\.conda\envs\seabreeze38\lib\site-packages\seabreeze\pyseabreeze\transport.py in list_devices(cls, **kwargs)
    275         try:
--> 276             pyusb_devices = usb.core.find(
    277                 find_all=True,

~\.conda\envs\seabreeze38\lib\site-packages\usb\core.py in find(find_all, backend, custom_match, **args)
   1262         else:
-> 1263             raise NoBackendError('No backend available')
   1264 

NoBackendError: No backend available

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-1-500825a1d47f> in <module>
     13 from seabreeze.spectrometers import list_devices, Spectrometer
     14 
---> 15 devices = list_devices()
     16 
     17 print (devices)

~\.conda\envs\seabreeze38\lib\site-packages\seabreeze\spectrometers.py in list_devices()
     32     if not hasattr(list_devices, "_api"):
     33         # noinspection PyProtectedMember
---> 34         list_devices._api = _lib.SeaBreezeAPI(**_lib._api_kwargs)
     35     # noinspection PyProtectedMember
     36     return list_devices._api.list_devices()

~\.conda\envs\seabreeze38\lib\site-packages\seabreeze\pyseabreeze\api.py in __init__(self, initialize, **_kwargs)
     54         self._kwargs = _kwargs  # allow passing additional kwargs to transports
     55         if initialize:
---> 56             self.initialize()
     57 
     58     def initialize(self):

~\.conda\envs\seabreeze38\lib\site-packages\seabreeze\pyseabreeze\api.py in initialize(self)
     62         it resets all usb devices on load
     63         """
---> 64         USBTransport.initialize(**self._kwargs)
     65 
     66     def shutdown(self):

~\.conda\envs\seabreeze38\lib\site-packages\seabreeze\pyseabreeze\transport.py in initialize(cls, **_kwargs)
    323     @classmethod
    324     def initialize(cls, **_kwargs):
--> 325         for device in cls.list_devices(**_kwargs):
    326             try:
    327                 device.pyusb_device.reset()

~\.conda\envs\seabreeze38\lib\site-packages\seabreeze\pyseabreeze\transport.py in list_devices(cls, **kwargs)
    282             )
    283         except usb.core.NoBackendError:
--> 284             raise RuntimeError("No pyusb backend found")
    285         # encapsulate
    286         for pyusb_device in pyusb_devices:

RuntimeError: No pyusb backend found

It really seems I have something setup incorrectly. I get errors when I run seabreeze_os_setup but I wonder if it is because I have run that in the past?

Install windows drivers? [y/n] y
Downloading windows drivers from github
Error when installing drivers
Press [enter] to close.

Hope this plethora of notes is helpful. enough for today. It really seems like it should be close.

Thanks. Dean

[ap--]

OK. If I understand your first point... the dark pixel issue is the reason I can't set True to Dark and nonlinearity correction in the get spectrum call and it is currently not fixed in version 1.2.0?

It's fixed in version 1.2.0 So if you are running 1.2.0 you should be able to set it to True and not crash with the error you reported before :)

Second, I'll transition to anaconda environments with python 3.8. Thanks!

Great. I have a suspicion that a possible download error will crash with a unspecific error message like you reported. Running it with python=3.8 should circumvent that. (It's totally possible that there's another bug though)

I think if I can get the dark part fixed I can patch the '4' setting temporarily but having py-seabreeze recognize Flame-S and have the trigger settings match would be great.

Yes. As soon as I have some spare time to continue and finish the work on "real" Flame-S support (not aliased as a USB2000plus) this will be supported out of the box.

Cheers, Andreas 😃

[waldowda]

I am not quite sure what happened but I stopped getting backend error on macOS. But then also discovered that the following seems to work after I modified devices.py to allow SINGLE_SHOT. I really doubt that did much for the backend USB error but...

print ("Stray Light Coef",spec.stray_light_coeffs)
print ("_nc: ", spec._nc)
print ("_dp: ", spec._dp)

data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=False)
data

wavelengths = spec.wavelengths()
#print ("Wavelengths: ", wavelengths)

wavelengths1 = wavelengths[24:2000]

data0b = data[24:2000] 

plt.plot(wavelengths1,data0b)
plt.show()

and then get:

Stray Light Coef <bound method DeprecatedSpectrometerMixin.stray_light_coeffs of <Spectrometer USB2000PLUS:FLMS16723>>
_nc:  None
_dp:  [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]

With dark=True and nc=False:

With dark =False and nc=False:

So, it seems perhaps that the problem is with the nonlinearity portion. When I switch back to cseabreeze I can easily grab those coef.s

Whenever correct_nonlinearity=True is set I still get:

---------------------------------------------------------------------------
SeaBreezeError                            Traceback (most recent call last)
<ipython-input-17-2246ae707de1> in <module>
      3 print ("_dp: ", spec._dp)
      4 
----> 5 data = spec.intensities(correct_dark_counts=True, correct_nonlinearity=True)
      6 data
      7 

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/spectrometers.py in intensities(self, correct_dark_counts, correct_nonlinearity)
    183             )
    184         if correct_nonlinearity and not self._nc:
--> 185             raise self._backend.SeaBreezeError(
    186                 "This device does not support nonlinearity correction."
    187             )

SeaBreezeError: This device does not support nonlinearity correction.

Still no idea why the backend USB issues stopped.

Hope this is not too much info and you find it useful. Regards, Dean

[ap--]

the backend issues probably stopped because you installed pyusb which is required for the pyseabreeze backend to work.

I'm not sure why it wasn't installed in the first place, but debugging issues with your local environment is almost impossible in retrospect. You would need to show every single command including output that you used to create the environment for me to be able to MAYBE figure out what's wrong with your python environment.

The spectra plot you showed are great! that means it's working already :+1: :medal_sports:

In other news: I just pushed the code required to let the pyseabreeze dynamicllay detect a flameS spectrometer. That means it's one step closer to having full flame-s support.

I also added the nonlinearity coefficient feature back into pyseabreeze for the USB2000+ and by extension the FlameS. Idk why it was missing there.

And the Triggermode 4 support is added to the FlameS for pyseabreeze, too.

So that means, the current master branch should make the FlameS work as expected. If you could test this, and there's no more issues I'll cut a new release.

Cheers, Andreas :smiley:

[waldowda]

Cool... 👏 All I did to install seabreeze was pip install seabreeze via terminal in the anaconda python3.8 environment I setup fresh. No dependencies were invoked as far as I could tell. It was the error that led me to pyusb. Should pyusb get added when installing seabreeze that way? I'll have to learn more about GitHub so I make sure I install the main branch. I'll try to test that out. For fun... here is a plot of an overlay of 53 absorbance spectra collected every 100 ms with 24 ave.s for a thin film of P3HT. Just testing. Without the non-linear correction... BTW I think trigger mode 4 should work for USB2000+ too ??? I don't have one though to test. I only have other USB650s. Will let you know.

[waldowda]

I installed what I think is the master branch. It didn't seem to be correct. The files have a current timestamp. I am still getting it assigned to USB2000+, don't see trigger 4, and nonlinear correction is not working. I must not have succeeded as I can see your changes on GitHub. Will see if I can figure out what I did wrong.

1.2.0
[<SeaBreezeDevice USB2000PLUS:FLMS16723>]
Serial Number:  FLMS16723
Max Intensity:  65535.0
Min. Int. Time:  1000
Stray Light Coef <bound method DeprecatedSpectrometerMixin.stray_light_coeffs of <Spectrometer USB2000PLUS:FLMS16723>>

Update

As a short check, I think I installed the proper master branch. I can now see the changed devices.py. BUT, it can't get a serial number now. I tried with its serial number and from first available.

import numpy as np
import time
import matplotlib.pyplot as plt

# explicitly request pyseabreeze
import seabreeze
#seabreeze.use('cseabreeze')
seabreeze.use('pyseabreeze')

print(seabreeze.__version__)

from seabreeze.spectrometers import list_devices, Spectrometer

devices = list_devices()

print (devices)

spec = Spectrometer.from_first_available()

spec

#spec = Spectrometer.from_serial_number("FLMS16723")

And got:

1.2.0.post7+g405b61a
[<SeaBreezeDevice USB2000PLUS:?>]
---------------------------------------------------------------------------
SeaBreezeError                            Traceback (most recent call last)
<ipython-input-8-6cb7e969c8f1> in <module>
     16 print (devices)
     17 
---> 18 spec = Spectrometer.from_first_available()
     19 
     20 spec

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/spectrometers.py in from_first_available(cls)
     89                 return cls(dev)
     90         else:
---> 91             raise cls._backend.SeaBreezeError("No unopened device found.")
     92 
     93     @classmethod

SeaBreezeError: No unopened device found.

Anaconda says that pyusb is installed... and I think 1.2.0.post7+g405b61a is the master branch. I used the following pip command in the appropriate environment.

 pip install git+git://github.com/ap--/python-seabreeze.git

Ideas?

[waldowda]

Also, I was trying to figure out why the serial number is not reported and I looked at the Flame S class. Why is nonlinearity in USB2000+ and not in Flame-S and the other Features are there?

class FLAMES(USB2000PLUS):

    model_name = "FLAMES"

    # spectrometer config
    dark_pixel_indices = DarkPixelIndices.from_ranges((6, 21))  # as in seabreeze-3.0.9
    integration_time_min = 1000
    integration_time_max = 655350000
    integration_time_base = 1
    spectrum_num_pixel = 2048
    spectrum_raw_length = (2048 * 2) + 1
    spectrum_max_value = 65535
    trigger_modes = TriggerMode.supported(
        "NORMAL", "SOFTWARE", "SYNCHRONIZATION", "HARDWARE", "SINGLE_SHOT"
    )

    # features
    feature_classes = (
        sbf.eeprom.SeaBreezeEEPromFeatureOOI,
        sbf.spectrometer.SeaBreezeSpectrometerFeatureUSB2000PLUS,
        sbf.continuousstrobe.SeaBreezeContinuousStrobeFeatureOOI,
        sbf.rawusb.SeaBreezeRawUSBBusAccessFeature,
    )

In USB2000+:

    # features
    feature_classes = (
        sbf.eeprom.SeaBreezeEEPromFeatureOOI,
        sbf.spectrometer.SeaBreezeSpectrometerFeatureUSB2000PLUS,
--->    sbf.nonlinearity.NonlinearityCoefficientsEEPromFeatureOOI,
        sbf.continuousstrobe.SeaBreezeContinuousStrobeFeatureOOI,
        sbf.rawusb.SeaBreezeRawUSBBusAccessFeature,
    )

[ap--]

Hi Dean,

the command you used is correct.

 pip install git+git://github.com/ap--/python-seabreeze.git

If you run it again now, your seabreeze version should show up as 1.2.0.post9+something

As you correctly noticed, I forgot to add the nonlinearity coefficient feature to the FlameS. And I pushed to more commits, fixing the issues.

Which OS are you running this on right now? Windows or Mac?

Cheers, Andreas 😃

[waldowda]

Good morning (here) (or evening... 😄 )... Thanks. I am currently running MacOS 10.15.6 for now just because my mac is my main box but when things are working will be transitioning to the Surface when installing the new build. I can move to the surface if that is more helpful.

FYI: I still don't get a serial number.

1.2.0.post9+g98f56cd
[<SeaBreezeDevice USB2000PLUS:?>]
---------------------------------------------------------------------------
SeaBreezeError                            Traceback (most recent call last)
<ipython-input-2-ba6e06943569> in <module>
     20 #spec
     21 
---> 22 spec = Spectrometer.from_serial_number("FLMS16723")
     23 
     24 print ("Serial Number: ", spec.serial_number)

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/spectrometers.py in from_serial_number(cls, serial)
    120                     return cls(dev)
    121         else:
--> 122             raise cls._backend.SeaBreezeError(
    123                 "No device attached with serial number '%s'." % serial
    124             )

SeaBreezeError: No device attached with serial number 'FLMS16723'.

Tried it again after forcing kernel to restart and rebooting Flame and get a different error?

1.2.0.post9+g98f56cd
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-1-b7c8313d4847> in <module>
     12 from seabreeze.spectrometers import list_devices, Spectrometer
     13 
---> 14 devices = list_devices()
     15 
     16 print (devices)

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/spectrometers.py in list_devices()
     34         list_devices._api = _lib.SeaBreezeAPI(**_lib._api_kwargs)
     35     # noinspection PyProtectedMember
---> 36     return list_devices._api.list_devices()
     37 
     38 

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/api.py in list_devices(self)
    102                 # opening the device will populate its serial number
    103                 try:
--> 104                     dev.open()
    105                 except USBTransportDeviceInUse:
    106                     # device used by another thread? -> exclude

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/devices.py in open(self)
    346         self._transport.open_device(self._raw_device)
    347         # substitute subclass if needed
--> 348         self.__class__ = self.__class__._substitute_compatible_subclass(self._transport)
    349         # cache features
    350         self._cached_features = {}

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/devices.py in _substitute_compatible_subclass(cls, transport)
    498 
    499         fpga = _FPGARegisterFeatureOOI(transport.protocol)
--> 500         if fpga.get_firmware_version()[0] >= 3:
    501             return FLAMES
    502         else:

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/features/fpga.py in get_firmware_version(self)
     31 
     32     def get_firmware_version(self):
---> 33         data = self.read_register(self.Codes.FIRMWARE_VERSION)
     34         fw_version = (
     35             (data >> 12) & 0x0F,  # major

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/features/fpga.py in read_register(self, register)
     23         fw_raw = self.protocol.query(0x6B, register)
     24         command, data = struct.unpack("<BH", fw_raw)
---> 25         assert command == self.Codes.FIRMWARE_VERSION
     26         return data
     27 

AssertionError: 

If I leave things alone and redo the import.... to list devices I am more or less back to the original error.

[ap--]

Hmmm... So the second error is interesting. Maybe fpga commands are handled differently on the FlameS... I just pushed a small update that add some more information to the AssertionError.

Please run the code that produces this error again, after you updated your seabreeze install. version should be 1.2.0.post10+something now.

[waldowda]

OK... Here is what happened:

1.2.0.post10+ge807a69
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-1-b7c8313d4847> in <module>
     12 from seabreeze.spectrometers import list_devices, Spectrometer
     13 
---> 14 devices = list_devices()
     15 
     16 print (devices)

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/spectrometers.py in list_devices()
     34         list_devices._api = _lib.SeaBreezeAPI(**_lib._api_kwargs)
     35     # noinspection PyProtectedMember
---> 36     return list_devices._api.list_devices()
     37 
     38 

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/api.py in list_devices(self)
    102                 # opening the device will populate its serial number
    103                 try:
--> 104                     dev.open()
    105                 except USBTransportDeviceInUse:
    106                     # device used by another thread? -> exclude

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/devices.py in open(self)
    346         self._transport.open_device(self._raw_device)
    347         # substitute subclass if needed
--> 348         self.__class__ = self.__class__._substitute_compatible_subclass(self._transport)
    349         # cache features
    350         self._cached_features = {}

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/devices.py in _substitute_compatible_subclass(cls, transport)
    498 
    499         fpga = _FPGARegisterFeatureOOI(transport.protocol)
--> 500         if fpga.get_firmware_version()[0] >= 3:
    501             return FLAMES
    502         else:

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/features/fpga.py in get_firmware_version(self)
     31 
     32     def get_firmware_version(self):
---> 33         data = self.read_register(self.Codes.FIRMWARE_VERSION)
     34         fw_version = (
     35             (data >> 12) & 0x0F,  # major

~/opt/anaconda3/envs/pyseabreeze/lib/python3.8/site-packages/seabreeze/pyseabreeze/features/fpga.py in read_register(self, register)
     23         fw_raw = self.protocol.query(0x6B, register)
     24         command, data = struct.unpack("<BH", fw_raw)
---> 25         assert command == self.Codes.FIRMWARE_VERSION, str(list(map(hex, fw_raw)))
     26         return data
     27 

AssertionError: ['0xfe', '0x55', '0x40']

Tried to build in win10 but git fails at building wheels.

[waldowda]

Here is what I have found which includes all of the register info around page 87 and the FPGA firmware version is at 0x04 read only though you likely have this.

https://www.oceaninsight.com/globalassets/catalog-blocks-and-images/manuals--instruction-old-logo/spectrometer/flameio.pdf

[ap--]

Yes. Could you please connect your FlameS via the OceanOptics Software and check its firmware version? If it's 4.5.5 (which I sadly doubt) we're lucky 😅

[waldowda]

OK... just came in from the garden. LOL. hold on. Was just looking up to see how to do that.

Update

Wow... they don't make it easy to find that info:

Host interface: Flame-S 4.02.0 FPGA: 4.05.5

I can't find any info on updates to firmware or firmware versions for the Flame-S.

[ap--]

Wow! Very nice! That means for some reason the spectrometer is just not adhering to the protocol specified in the datasheet...

I need to fix the seabreeze.pyseabreeze.features.fpga submodule. But in the meantime, you should be able to disable the assertion check (which was just added as a sanity check while implementing the functionality) by doing the following:

Run your python script that you're using to test the spectrometer not with

python your-spectrometer-test-script.py

But with:

python -O your-spectrometer-test-script.py

(That is a capital O for optimize, which ignores all assert statements in the python code at runtime)

[waldowda]

I have been testing in jupyter notebooks and am not sure how to do that in anaconda/jupyter. I'll research that or I'll put the cells together as a single .py and test from a python call. I think I can do that. I am still 'learning to really drive' anaconda. I won't likely get to that until tomorrow now.

I was able to go back to the plain version and added the line for nonlinearity. It then functions albeit without native acknowledgment of being a Flame-S but it 'appears' to function for now with dark correction, nonlinearity, and trigger mode 4.

You must have found out info about upgraded firmware. I could not find any info on that. Do you think I should ask OI for an update to the firmware?

Will let you know what I find. Thanks!

[ap--]

Hi Dean, could you please try with the newest version? 1.2.0.post11+something

[waldowda]

UPDATE

Nice! Here is the result:

1.2.0.post11+g6fa09df
[<SeaBreezeDevice FLAMES:FLMS16723>]

Everything I have tried worked in a new environment. I pre-installed pyusb in case it didn't grab it. I'll test a bit more but looks great for these issues! Congrats! I should include that both dark and nonlinearity worked as did trigger 4.

I work on developing the spectroelectrochemistry application now. I will still look at the jump in acquisition time / integration time with increasing integration time. I suspect that may be a spectrometer issue?

[ap--]

No rush. Will only be able to have another look tomorrow evening. Cheers 😴

[ap--]

Awesome 🎉 🥳 Thanks for your help and patience 🥇 😃

Okay, I'll try to get a new version out on the weekend. I'll close the two issues and will open one specifically for the timing issue. But yes, this might be a spectrometer issue.

Cheers, Andreas 😃

[waldowda]

Thanks Andreas! I'll look at the new issue and can maybe contribute the code I used with some tweaks. I am sure you can generate testing code that is better than mine. LOL. Best wishes. Dean