if there is no picked coordinates pyseg -picking protocol fails

[Vilax]

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]

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]

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.