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scipion-em / scipion-em-pyseg

Plugin to use PySeg programs within the Scipion framework
GNU General Public License v3.0
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if there is no picked coordinates pyseg -picking protocol fails #71

Open Vilax opened 1 year ago

Vilax commented 1 year ago

00001: project._getRelationGraph: parent Node is None: 786 00002: project._getRelationGraph: parent Node is None: 786 00003: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:35: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00004: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00005: eps=np.finfo(np.float).eps, 00006: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:597: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00007: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00008: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True, 00009: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:836: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00010: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00011: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True, 00012: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:862: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00013: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00014: eps=np.finfo(np.float).eps, positive=False): 00015: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1097: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00016: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00017: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps, 00018: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1344: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00019: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00020: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps, 00021: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1480: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00022: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00023: eps=np.finfo(np.float).eps, copy_X=True, positive=False): 00024: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:152: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00025: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00026: precompute=False, eps=np.finfo(np.float).eps, 00027: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:320: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00028: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00029: eps=np.finfo(np.float).eps, random_state=None, 00030: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:580: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00031: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00032: eps=4 np.finfo(np.float).eps, n_jobs=None, 00033: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/decomposition/online_lda.py:31: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00034: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00035: EPS = np.finfo(np.float).eps 00036: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:35: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00037: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00038: eps=np.finfo(np.float).eps, 00039: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:597: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00040: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00041: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True, 00042: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:836: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00043: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00044: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True, 00045: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:862: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00046: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00047: eps=np.finfo(np.float).eps, positive=False): 00048: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1097: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00049: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00050: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps, 00051: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1344: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00052: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00053: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps, 00054: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1480: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00055: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00056: eps=np.finfo(np.float).eps, copy_X=True, positive=False): 00057: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:152: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00058: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00059: precompute=False, eps=np.finfo(np.float).eps, 00060: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:320: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00061: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00062: eps=np.finfo(np.float).eps, random_state=None, 00063: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:580: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00064: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00065: eps=4 np.finfo(np.float).eps, n_jobs=None, 00066: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/decomposition/online_lda.py:31: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00067: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00068: EPS = np.finfo(np.float).eps 00069: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:35: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00070: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00071: eps=np.finfo(np.float).eps, 00072: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:597: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00073: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00074: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True, 00075: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:836: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00076: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00077: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True, 00078: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:862: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00079: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00080: eps=np.finfo(np.float).eps, positive=False): 00081: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1097: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00082: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00083: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps, 00084: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1344: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00085: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00086: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps, 00087: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1480: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00088: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00089: eps=np.finfo(np.float).eps, copy_X=True, positive=False): 00090: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:152: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00091: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00092: precompute=False, eps=np.finfo(np.float).eps, 00093: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:320: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00094: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00095: eps=np.finfo(np.float).eps, random_state=None, 00096: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:580: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00097: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00098: eps=4 np.finfo(np.float).eps, n_jobs=None, 00099: /home/tomo/anaconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/decomposition/online_lda.py:31: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. 00100: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 00101: EPS = np.finfo(np.float).eps 00102: project._getRelationGraph: parent Node is None: 786 00103: project._getRelationGraph: parent Node is None: 786 00104: Couldn't run the code in a thread. 00105: Traceback (most recent call last): 00106: File "/home/tomo/scipion3/scipion-pyworkflow/pyworkflow/protocol/executor.py", line 148, in run 00107: self.step._run() # not self.step.run() , to avoid race conditions 00108: File "/home/tomo/scipion3/scipion-pyworkflow/pyworkflow/protocol/protocol.py", line 255, in _run 00109: resultFiles = self._runFunc() 00110: File "/home/tomo/scipion3/scipion-pyworkflow/pyworkflow/protocol/protocol.py", line 251, in _runFunc 00111: return self._func(self._args) 00112: File "/home/tomo/scipion3/Plugins/scipion-em-pyseg/pyseg/protocols/protocol_picking.py", line 194, in createOutputStep 00113: raise Exception('ERROR! No coordinates were picked.') 00114: Exception: ERROR! No coordinates were picked. 00115: Protocol failed: ERROR! No coordinates were picked.

JorMaister commented 1 year ago

Yes, that error is thrown by us. We thought it should fail with that "ERROR! No coordinates were picked" message as there's no sense in a green protocol without particles picked. Do you have any suggestions regarding that?

Vilax commented 1 year ago

The thing is that the most probable source of the error is the graph or the fils. I would suggest to check that protocols, because the problem would be in that protocol not in the picking. I would raise the error or do the validation in the fil/graphs. The picking is not failing.