Error while running

[farazmoradi]

Hi, I received this error while running Phy on some of the sorted data!

QWidget: Must construct a QApplication before a QWidget zsh: abort phy template-gui params.py

[hstern2]

I'm also seeing this error... any suggestions?

$ phy template-gui params.py

File "/software/miniconda3/4.9.2/envs/phy2/lib/python3.7/site-packages/phylib/io/model.py", line 475, in _read_array raise IOError() OSError

QWidget: Must construct a QApplication before a QWidget Aborted (core dumped)

[guitchounts]

I'm seeing a similar error after installing phy using the Developer instructions in the Readme. Has anyone seen anything like this and solved it?

`(phy) [gg121@compute-e-16-229 phylib]$ phy template-gui /n/groups/datta/guitchounts/data/gmou48/gmou48_2021-12-11_14-24-38_odor/tmp_MS4/phy/params.py 16:41:57.386 [W] model:1325 File /n/groups/datta/guitchounts/data/gmou48/gmou48_2021-12-11_14-24-38_odor/tmp_MS4/phy/None does not exist. 16:41:59.642 [E] init:62 An error has occurred (AssertionError): Traceback (most recent call last): File "/home/gg121/anaconda3/envs/phy/bin/phy", line 33, in sys.exit(load_entry_point('phy', 'console_scripts', 'phy')()) File "/home/gg121/anaconda3/envs/phy/lib/python3.8/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/home/gg121/anaconda3/envs/phy/lib/python3.8/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/home/gg121/anaconda3/envs/phy/lib/python3.8/site-packages/click/core.py", line 1659, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/gg121/anaconda3/envs/phy/lib/python3.8/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/gg121/anaconda3/envs/phy/lib/python3.8/site-packages/click/core.py", line 754, in invoke return __callback(args, *kwargs) File "/home/gg121/anaconda3/envs/phy/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func return f(get_current_context(), args, kwargs) File "/home/gg121/code/phy/phy/apps/init.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "/home/gg121/code/phy/phy/apps/template/gui.py", line 209, in template_gui model = load_model(params_path) File "/home/gg121/code/phylib/phylib/io/model.py", line 1350, in load_model return TemplateModel(**get_template_params(params_path)) File "/home/gg121/code/phylib/phylib/io/model.py", line 339, in init self._load_data() File "/home/gg121/code/phylib/phylib/io/model.py", line 358, in _load_data assert self.amplitudes.shape == (ns,) AssertionError

QWidget: Must construct a QApplication before a QWidget Aborted`

[schloegl]

I saw the same issue. In my case, it was cased by an incorrect params.py, with an entry for n_channels_dat that did not match the data.

Part of the problem here is, the program aborts without a meaningful error message. In order to address this, I've applied this patch

diff --git a/phylib/io/model.py b/phylib/io/model.py
index ad008f5..e755bc9 100644
--- a/phylib/io/model.py
+++ b/phylib/io/model.py
@@ -380,6 +380,9 @@ class TemplateModel(object):
         self.channel_mapping = self._load_channel_map()
         self.n_channels = nc = self.channel_mapping.shape[0]
         if self.n_channels_dat:
+            if not np.all(self.channel_mapping <= self.n_channels_dat - 1):
+                print("channel miss-match, check n_channels_dat in your params file %d,%d\n",self.channel_mapping,self.n_channels_dat)
+                return
             assert np.all(self.channel_mapping <= self.n_channels_dat - 1)

         # Channel positions.

[fredbarthelemy]

Hi, I face a similar issue when I try to run phy.

Traceback (most recent call last): File "D:\Labo\Anaconda\envs\phy_environment\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "D:\Labo\Anaconda\envs\phy_environment\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "D:\Labo\Anaconda\envs\phy_environment\Scripts\phy.exe__main.py", line 7, in sys.exit(phycli()) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\click\core.py", line 1130, in call return self.main(args, kwargs) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\click\core.py", line 1055, in main rv = self.invoke(ctx) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\click\core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\click\core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\click\core.py", line 760, in invoke return __callback(args, *kwargs) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\click\decorators.py", line 26, in new_func return f(get_current_context(), args, **kwargs) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\phy\apps\init.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\phy\apps\template\gui.py", line 209, in template_gui model = load_model(params_path) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\phylib\io\model.py", line 1433, in load_model return TemplateModel(get_template_params(params_path)) File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\phylib\io\model.py", line 339, in init__ self._load_data() File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\phylib\io\model.py", line 404, in _load_data self.sparse_templates = self._load_templates() File "D:\Labo\Anaconda\envs\phy_environment\lib\site-packages\phylib\io\model.py", line 701, in _load_templates assert data.dtype in (np.float32, np.float64) AssertionError

I tried the patch proposed by @schloegl but it doesn't change anything in my case.

Regards

[fredbarthelemy]

Hi again,

I solved the issue. It was due to an incorrect data format using spike interface pipeline to manage the sorting. Now I scale the data and convert from int16 to float32 and it's just fine.

Best

[jessiburd]

I got the same error. When I try to debug, I get the following output. Does anyone know what the problem is?

(phy2) C:\Users\12023\Desktop\Ephys\Data\Lav74-M\Spikesorting_results\P1_BOS> phy template-gui params.py --debug 14:42:33.663 [D] init:68 Start capturing exceptions. 14:42:33.740 [W] model:603 Unreferenced clusters found in templates (generally not a problem) 14:42:33.779 [D] model:619 Loading spike clusters. 14:42:33.820 [W] model:625 Unreferenced clusters found in spike_clusters (generally not a problem) 14:42:33.867 [E] init:62 An error has occurred (AssertionError): Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "C:\Users\12023\anaconda3\envs\phy2\Scripts\phy.exe__main.py", line 7, in sys.exit(phycli()) ^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\click\core.py", line 1157, in call return self.main(*args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\click\core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\click\core.py", line 783, in invoke return callback(*args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\click\decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\phy\apps__init__.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\phy\apps\template\gui.py", line 209, in template_gui model = load_model(params_path) ^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\phylib\io\model.py", line 1433, in load_model return TemplateModel(**get_template_params(params_path)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\phylib\io\model.py", line 339, in init self._load_data() File "C:\Users\12023\anaconda3\envs\phy2\Lib\site-packages\phylib\io\model.py", line 383, in _load_data assert np.all(self.channel_mapping <= self.n_channels_dat - 1) AssertionError

[LordKelv]

Hi again,

I solved the issue. It was due to an incorrect data format using spike interface pipeline to manage the sorting. Now I scale the data and convert from int16 to float32 and it's just fine.

Best

Hey there Fred! How did you scale the data and convert from int16 to float32? Thanks, Kelvin