Problem installing due to tests.various module missing

[tkjmk]

Hello!

Thanks for making larvaworld! I would love to try it to simulate larval movement (to compare movement to my own behavioural assays). I have followed all the installation steps. Only additional step was installing the 'siunits' module myself. This is all with python3.7.7.

I am trying to run some of the example lines from the README.txt (specifically the lines related to larvaworld_gui.py and batch_run.py)

When running any of the scripts I run into an error:

Traceback (most recent call last):
  File "larvaworld_gui.py", line 11, in <module>
    from lib.gui.tabs.gui import LarvaworldGui
  File "../lib/gui/tabs/gui.py", line 10, in <module>
    from lib.gui.tabs import intro_tab, model_tab, life_tab, sim_tab, batch_tab, essay_tab, import_tab, \
  File "../lib/gui/tabs/sim_tab.py", line 11, in <module>
    from run.exec_run import Exec
  File "../run/exec_run.py", line 10, in <module>
    from lib.sim.batch.functions import retrieve_results
  File "../lib/sim/batch/functions.py", line 15, in <module>
    from lib.sim.single.single_run import SingleRun
  File "../lib/sim/single/single_run.py", line 8, in <module>
    from lib.model.envs._larvaworld_sim import LarvaWorldSim
  File "../lib/model/envs/_larvaworld_sim.py", line 9, in <module>
    from lib.model.envs._larvaworld import LarvaWorld, generate_larvae, get_sample_bout_distros, sample_group
  File "../lib/model/envs/_larvaworld.py", line 30, in <module>
    import tests.various.gui.dtype_dicts as dtypes
ModuleNotFoundError: No module named 'tests.various'

I'm unsure whether this is meant to be part of a module called tests - which I did make sure I have. That made me think that it might be a missing directory/script that is meant to be downloaded with larvaworld. I've tried on both linux and mac (same error is raised).

Do you have any ideas on how I could get past this error?

Thanks again! TK

[bagjohn]

Hello TK

Thanks for your interest. Yes there is a line there that should not exist. The tests module should not be required. Please download the github code again. Let me know if you encounter further issues.

Panos

Στις Δευ, 18 Οκτ 2021 στις 4:53 μ.μ., ο/η TK @.***> έγραψε:

Hello!

Thanks for making larvaworld! I would love to try it to simulate larval movement (to compare movement to my own behavioural assays). I have followed all the installation steps. Only additional step was installing the 'siunits' module myself. This is all with python3.7.7.

I am trying to run some of the example lines from the README.txt (specifically the lines related to larvaworld_gui.py and batch_run.py)

When running any of the scripts I run into an error:

Traceback (most recent call last): File "larvaworld_gui.py", line 11, in from lib.gui.tabs.gui import LarvaworldGui File "../lib/gui/tabs/gui.py", line 10, in from lib.gui.tabs import intro_tab, model_tab, life_tab, sim_tab, batch_tab, essay_tab, import_tab, \ File "../lib/gui/tabs/sim_tab.py", line 11, in from run.exec_run import Exec File "../run/exec_run.py", line 10, in from lib.sim.batch.functions import retrieve_results File "../lib/sim/batch/functions.py", line 15, in from lib.sim.single.single_run import SingleRun File "../lib/sim/single/single_run.py", line 8, in from lib.model.envs._larvaworld_sim import LarvaWorldSim File "../lib/model/envs/_larvaworld_sim.py", line 9, in from lib.model.envs._larvaworld import LarvaWorld, generate_larvae, get_sample_bout_distros, sample_group File "../lib/model/envs/_larvaworld.py", line 30, in import tests.various.gui.dtype_dicts as dtypesModuleNotFoundError: No module named 'tests.various'

I'm unsure whether this is meant to be part of a module called tests - which I did make sure I have. That made me think that it might be a missing directory/script that is meant to be downloaded with larvaworld. I've tried on both linux and mac (same error is raised).

Do you have any ideas on how I could get past this error?

Thanks again! TK

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[tkjmk]

Thank you very much Panos! That worked for downloading. I now noticed that the examples do not work.

For example:

I ran
python batch_run.py odor_pref -N 25 -t 3.0 -rng -200.0 200.0 -Ngrd 5 I then got the error:

batch_run.py: error: argument batch: invalid choice: 'odor_pref' (choose from 'chemotaxis_approach', 'chemotaxis_local', 'PItest_off', 'PItrain_mini', 'PItrain', 'patchy_food', 'food_grid', 'growth', 'RvsS', 'imitation', 'tactile_detection')

so I changed it to patchy food: i.e. python batch_run.py patchy_food -N 25 -t 3.0 -rng -200.0 200.0 -Ngrd 5

I then get

Traceback (most recent call last):
  File "batch_run.py", line 43, in <module>
    space_kwargs[k] = batch_conf['space_search'][k]
KeyError: 'pars'

This error happens for other keys I tried too like 'chemotaxis_approach'.

---

I also tried: python exp_run.py dispersion -N 30 -t 3.0 -img -a

I got the error message: exp_run.py: error: unrecognized arguments: -N 30 -img

I then changed -img to -m image, and did not find an appropriate replacement for -N30. Running: python exp_run.py dispersion -t 3.0 -m image -a gave me the follwoing error:

Traceback (most recent call last):
  File "exp_run.py", line 24, in <module>
    ds = SingleRun(**exp_conf, vis_kwargs=d['visualization']).run()
  File "../lib/sim/single/single_run.py", line 57, in __init__
    save_to=self.d.vis_dir, **kwargs)
  File "../lib/model/envs/_larvaworld_sim.py", line 24, in __init__
    self.create_larvae(larva_groups=self.larva_groups, parameter_dict=parameter_dict)
  File "../lib/model/envs/_larvaworld_sim.py", line 94, in create_larvae
    sample_dict = sample_group(sample, N, self.sample_ps)
  File "../lib/model/envs/_larvaworld.py", line 675, in sample_group
    d = LarvaDataset(sample['dir'], load_data=False)
  File "../lib/stor/larva_dataset.py", line 22, in __init__
    self.define_paths(dir)
  File "../lib/stor/larva_dataset.py", line 635, in define_paths
    os.makedirs(v, exist_ok=True)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  [Previous line repeated 4 more times]
  File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 45] Operation not supported: '/home/panos'

I think there is a path hard coded.

---

I also could not find process.py, I guess it is now exec_run.py

Would you prefer if I opened these in another ticket?

These errors also occur from the lines in the tutorials.

The first goal I have is to be able to simulate x third instar larva on a 1000x1000px grid for 20 minutes (sampling their coordinates at either 1 or 10 fps).

Thanks again! Tane

[bagjohn]

Hello Tane and thanks again for your patience

Indeed the terminal executables are somewhat obsolete because of the GUI. Especially importing experimental data is much more transparent there. Did you manage to launch the GUI by python larvaworld_gui.py?

Στις Δευ, 18 Οκτ 2021 στις 11:40 μ.μ., ο/η TK @.***> έγραψε:

Thank you very much Panos! That worked for downloading. I now noticed that the examples do not work.

For example:

I ran python batch_run.py odor_pref -N 25 -t 3.0 -rng -200.0 200.0 -Ngrd 5 I then got the error:

batch_run.py: error: argument batch: invalid choice: 'odor_pref' (choose from 'chemotaxis_approach', 'chemotaxis_local', 'PItest_off', 'PItrain_mini', 'PItrain', 'patchy_food', 'food_grid', 'growth', 'RvsS', 'imitation', 'tactile_detection')

so I changed it to patchy food: i.e. python batch_run.py patchy_food -N 25 -t 3.0 -rng -200.0 200.0 -Ngrd 5

I then get

Traceback (most recent call last): File "batch_run.py", line 43, in space_kwargs[k] = batch_conf['space_search'][k]KeyError: 'pars'

This error happens for other keys I tried too like 'chemotaxis_approach'.

I also tried: python exp_run.py dispersion -N 30 -t 3.0 -img -a

I got the error message: exp_run.py: error: unrecognized arguments: -N 30 -img

I then changed -img to -m image, and did not find an appropriate replacement for -N30. Running: python exp_run.py dispersion -t 3.0 -m image -a gave me the follwoing error:

Traceback (most recent call last): File "exp_run.py", line 24, in ds = SingleRun(exp_conf, vis_kwargs=d['visualization']).run() File "../lib/sim/single/single_run.py", line 57, in init save_to=self.d.vis_dir, kwargs) File "../lib/model/envs/_larvaworld_sim.py", line 24, in init self.create_larvae(larva_groups=self.larva_groups, parameter_dict=parameter_dict) File "../lib/model/envs/_larvaworld_sim.py", line 94, in create_larvae sample_dict = sample_group(sample, N, self.sample_ps) File "../lib/model/envs/_larvaworld.py", line 675, in sample_group d = LarvaDataset(sample['dir'], load_data=False) File "../lib/stor/larva_dataset.py", line 22, in init self.define_paths(dir) File "../lib/stor/larva_dataset.py", line 635, in define_paths os.makedirs(v, exist_ok=True) File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 213, in makedirs makedirs(head, exist_ok=exist_ok) File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 213, in makedirs makedirs(head, exist_ok=exist_ok) File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 213, in makedirs makedirs(head, exist_ok=exist_ok) [Previous line repeated 4 more times] File "/usr/local/Caskroom/miniconda/base/lib/python3.7/os.py", line 223, in makedirs mkdir(name, mode)OSError: [Errno 45] Operation not supported: '/home/panos'

I think there is a path hard coded.

I also could not find process.py, I guess it is now exec_run.py

Would you prefer if I opened these in another ticket?

These errors also occur from the lines in the tutorials.

The first goal I have is to be able to simulate x third instar larva on a 1000x1000px grid for 20 minutes (sampling their coordinates at either 1 or 10 fps).

Thanks again! Tane

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nawrotlab/larvaworld/issues/1#issuecomment-946189224, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABTJYJJZ3ZDB33BQWN4TJODUHSH45ANCNFSM5GG3L3TQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[tkjmk]

Hey,

I did manage to run the GUI. Although, I could not view any of the tutorial videos.

On the video tab I can click the images and watch the videos, however whenever I go to the tutorial tab it does not work (nor on the opening page of the GUI).

The only mp4 files I have in the larvaworld directory is cockatoo.mp4 and realshort.mp4.

The only difference I directly see that might be causing that is that lib/gui/tabs/video_tab.py has a line in the build function that says:

link0 = "http://computational-systems-neuroscience.de/wp-content/uploads/2021/04/"

whereas lib/gui/tabs/tutorial_tab.py does not have that line.

I did try playing around with the different tabs on the GUI, but I haven't managed to get any simulations yet. I will try some more and hopefully be able to run it after the tutorial videos. In the end it would be easier for me to run it through command line as I want to run the simulations as part of a pipeline (I would run 100s (to 1000s) of simulations in the end).

[bagjohn]

Hey! Indeed the tutorial videos are not working. This is in the todo list. You should be able to run simulations via the tabs 'simulation', 'batch_run', 'essay'. If you want to alos see them go to settings tab and set mode to video. The command line currently works for single simulations (exp_run.py). The batch_run.py will also work but with less available flags than mentioned in the tutorial notebook.

Let me know how it goes!

Panos

[tkjmk]

Hey,

I am still unable to run simulations even through the gui. To use mode: video, I had to install imageio-ffmpeg, python -m pip install imageio_ffmpeg

I tried each of the tabs ('simulation', 'batch_run', and 'essay'), each of them gave different errors. I was not able to successfully run the simulation on any of them (errors raised on each).

For example, when I run the 'batch_run' tab. I leave everything default. I just change the first drop down to 'PItest_off' (the simulation drop down also changes to 'PItest_off' automatically)

Hello from the pygame community. https://www.pygame.org/contribute.html
* Error performing wm_overrideredirect *
MainProcess pypet.storageservice.HDF5StorageService INFO     I will use the hdf5 file `larvaworld/data/SimGroup/batch_runs/PItest_off/PItest_off.hdf5`.
MainProcess pypet.environment.Environment INFO     Environment initialized.
Created novel environment
MainProcess pypet.naturalnaming.NaturalNamingInterface ERROR    Failed adding `ranges` under ``.
Traceback (most recent call last):
  File "larvaworld/run/exec_run.py", line 90, in <module>
    k.exec_run()
  File "larvaworld/run/exec_run.py", line 78, in exec_run
    res = batch_run(**batch_kwargs)
  File "../lib/sim/batch/batch.py", line 48, in batch_run
    return _batch_run(**kwargs)
  File "../lib/sim/batch/batch.py", line 154, in _batch_run
    env =test_batch()
  File "../lib/sim/batch/batch.py", line 147, in test_batch
    space=space, **env_kws)
  File "../lib/sim/batch/batch.py", line 59, in get_batch_env
    traj = config_traj(traj, optimization, batch_methods)
  File "../lib/sim/batch/aux.py", line 23, in config_traj
    traj.f_aconf(k, v)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/naturalnaming.py", line 3624, in f_add_config
    args=args, kwargs=kwargs)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/naturalnaming.py", line 1230, in _add_generic
    constructor, args, kwargs)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/naturalnaming.py", line 1331, in _add_to_tree
    args, kwargs)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/naturalnaming.py", line 1612, in _create_any_param_or_result
    instance = root._construct_instance(constructor, full_name, *args, **kwargs)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/trajectory.py", line 3223, in _construct_instance
    return constructor(full_name, *args, **kwargs)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/parameter.py", line 733, in __init__
    self.f_set(data)
  File "larvaworld/larvaworld_venv/lib/python3.7/site-packages/pypet/parameter.py", line 951, in f_set
    'tuple or list.' % (str(data), str(type(data))))
TypeError: Unsupported data `[]` of type `<class 'numpy.ndarray'>`. If you passed a tuple or list, this error might also be caused by heterogeneous data within the tuple or list.

Also when I try other settings such as patchy_food the problem is: larvaworld/data/SimGroup/batch_runs directory is missing so the hdf5 files (e.g. patchy_food.hdf5 is not found).

When I try to run batch_runs.py on the command line, the error I get is always - no matter the line:

Traceback (most recent call last):
  File "batch_run.py", line 43, in <module>
    space_kwargs[k] = batch_conf['space_search'][k]
KeyError: 'pars'

If you have any solutions to how I could get that running, please let me know. it would be helpful to be able to run the batch_runs.py to simulate the movement of larvae without any attractors.

Best, TK