config_checker update and linting for C408,C419,C405, C409, E721,F401,E722

py4DSTEM/braggvectors/braggvectors.py

@@ -1,7 +1,7 @@
 # Defines the BraggVectors class
 
 from py4DSTEM.data import Data
-from emdfile import Custom, PointListArray, PointList, Metadata
+from emdfile import Custom, PointListArray, Metadata
 from py4DSTEM.braggvectors.braggvector_methods import BraggVectorMethods
 from os.path import basename
 import numpy as np

py4DSTEM/braggvectors/diskdetection.py

@@ -221,7 +221,7 @@ def find_Bragg_disks(
                 mode = "dp"
             elif data.ndim == 3:
                 mode = "dp_stack"
-        except:
+        except Exception:
             er = f"entry {data} for `data` could not be parsed"
             raise Exception(er)
 

py4DSTEM/braggvectors/diskdetection_aiml.py

@@ -4,16 +4,13 @@
 """
 
 import os
-import glob
 import json
 import shutil
 import numpy as np
 
-from scipy.ndimage import gaussian_filter
 from time import time
-from numbers import Number
 
-from emdfile import tqdmnd, PointList, PointListArray
+from emdfile import tqdmnd
 from py4DSTEM.braggvectors.braggvectors import BraggVectors
 from py4DSTEM.data import QPoints
 from py4DSTEM.process.utils import get_maxima_2D
@@ -103,12 +100,12 @@ def find_Bragg_disks_aiml_single_DP(
     """
     try:
         import crystal4D
-    except:
+    except ModuleNotFoundError:
         raise ImportError("Import Error: Please install crystal4D before proceeding")
     try:
         import tensorflow as tf
-    except:
-        raise ImportError(
+    except ModuleNotFoundError:
+        raise ModuleNotFoundError(
             "Please install tensorflow before proceeding - please check "
             + "https://www.tensorflow.org/install"
             + "for more information"
@@ -256,7 +253,7 @@ def find_Bragg_disks_aiml_selected(
 
     try:
         import crystal4D
-    except:
+    except ModuleNotFoundError:
         raise ImportError("Import Error: Please install crystal4D before proceeding")
 
     assert len(Rx) == len(Ry)
@@ -433,7 +430,7 @@ def find_Bragg_disks_aiml_serial(
 
     try:
         import crystal4D
-    except:
+    except ModuleNotFoundError:
         raise ImportError("Import Error: Please install crystal4D before proceeding")
 
     # Make the peaks PointListArray
@@ -559,7 +556,7 @@ def find_Bragg_disks_aiml(
     model_path=None,
     distributed=None,
     CUDA=True,
-    **kwargs
+    **kwargs,
 ):
     """
     Finds the Bragg disks in all diffraction patterns of datacube by AI/ML method. This method
@@ -643,8 +640,8 @@ def find_Bragg_disks_aiml(
     """
     try:
         import crystal4D
-    except:
-        raise ImportError("Please install crystal4D before proceeding")
+    except ModuleNotFoundError:
+        raise ImportError("Import Error: Please install crystal4D before proceeding")
 
     def _parse_distributed(distributed):
         import os
@@ -840,7 +837,8 @@ def _integrate_disks(DP, maxima_x, maxima_y, maxima_int, int_window_radius=1):
         disks.append(np.average(disk))
     try:
         disks = disks / max(disks)
-    except:
+    # TODO work out what exception would go here
+    except Exception:
         pass
     return (maxima_x, maxima_y, disks)
 
@@ -878,8 +876,8 @@ def _get_latest_model(model_path=None):
 
     try:
         import tensorflow as tf
-    except:
-        raise ImportError(
+    except ModuleNotFoundError:
+        raise ModuleNotFoundError(
             "Please install tensorflow before proceeding - please check "
             + "https://www.tensorflow.org/install"
             + "for more information"
@@ -891,8 +889,12 @@ def _get_latest_model(model_path=None):
     if model_path is None:
         try:
             os.mkdir("./tmp")
-        except:
+        except FileExistsError:
+            pass
+        except Exception as e:
+            # TODO work out if I want to pass or raise
             pass
+            # raise e
         # download the json file with the meta data
         download_file_from_google_drive("FCU-Net", "./tmp/model_metadata.json")
         with open("./tmp/model_metadata.json") as f:
@@ -905,7 +907,10 @@ def _get_latest_model(model_path=None):
             with open("./tmp/model_metadata_old.json") as f_old:
                 metaold = json.load(f_old)
                 file_id_old = metaold["file_id"]
-        except:
+        # TODO Double check this is correct Error
+        except FileNotFoundError:
+            file_id_old = file_id
+        except Exception:
             file_id_old = file_id
 
         if os.path.exists(file_path) and file_id == file_id_old:
@@ -921,7 +926,8 @@ def _get_latest_model(model_path=None):
             download_file_from_google_drive(file_id, filename)
             try:
                 shutil.unpack_archive(filename, "./tmp", format="zip")
-            except:
+            # TODO Work work what specific exception
+            except Exception:
                 pass
             model_path = file_path
             os.rename("./tmp/model_metadata.json", "./tmp/model_metadata_old.json")

py4DSTEM/braggvectors/diskdetection_aiml_cuda.py

@@ -8,8 +8,7 @@
 
 from emdfile import tqdmnd
 from py4DSTEM.braggvectors.braggvectors import BraggVectors
-from emdfile import PointList, PointListArray
-from py4DSTEM.data import QPoints
+from emdfile import PointList
 from py4DSTEM.braggvectors.kernels import kernels
 from py4DSTEM.braggvectors.diskdetection_aiml import _get_latest_model
 
@@ -22,8 +21,8 @@
 
 try:
     import tensorflow as tf
-except:
-    raise ImportError(
+except ModuleNotFoundError:
+    raise ModuleNotFoundError(
         "Please install tensorflow before proceeding - please check "
         + "https://www.tensorflow.org/install"
         + "for more information"
@@ -265,7 +264,7 @@ def _find_Bragg_disks_aiml_single_DP_CUDA(
     blocks=None,
     threads=None,
     model_path=None,
-    **kwargs
+    **kwargs,
 ):
     """
     Finds the Bragg disks in single DP by AI/ML method. This method utilizes FCU-Net
@@ -637,7 +636,8 @@ def upsampled_correlation_cp(imageCorr, upsampleFactor, xyShift):
         )
         dx = (icc[2, 1] - icc[0, 1]) / (4 * icc[1, 1] - 2 * icc[2, 1] - 2 * icc[0, 1])
         dy = (icc[1, 2] - icc[1, 0]) / (4 * icc[1, 1] - 2 * icc[1, 2] - 2 * icc[1, 0])
-    except:
+    # TODO I think this is just the IndexError
+    except Exception:
         dx, dy = (
             0,
             0,
@@ -733,6 +733,7 @@ def _integrate_disks_cp(DP, maxima_x, maxima_y, maxima_int, int_window_radius=1)
         disks.append(np.average(disk))
     try:
         disks = disks / max(disks)
-    except:
+    # TODO work out what exception to use, ZeroDivisionError
+    except Exception:
         pass
     return (maxima_x, maxima_y, disks)

py4DSTEM/braggvectors/diskdetection_cuda.py

@@ -618,7 +618,8 @@ def upsampled_correlation(imageCorr, upsampleFactor, xyShift):
             dy = (icc[1, 2] - icc[1, 0]) / (
                 4 * icc[1, 1] - 2 * icc[1, 2] - 2 * icc[1, 0]
             )
-        except:
+        # TODO Work out what exception to use  IndexError
+        except Exception:
             dx, dy = (
                 0,
                 0,

py4DSTEM/braggvectors/diskdetection_parallel_new.py

@@ -1,24 +1,16 @@
 import numpy as np
-import matplotlib.pyplot as plt
-import h5py
-import time
 import dill
 
 import dask
 import dask.array as da
 import dask.config
 from dask import delayed
 from dask.distributed import Client, LocalCluster
-from dask.diagnostics import ProgressBar
 
-# import dask.bag as db
-
-# import distributed
 from distributed.protocol.serialize import register_serialization_family
 import distributed
 
-import py4DSTEM
-from emdfile import PointListArray, PointList
+from emdfile import PointListArray
 from py4DSTEM.braggvectors.diskdetection import _find_Bragg_disks_single_DP_FK
 
 
@@ -100,7 +92,7 @@ def beta_parallel_disk_detection(
     close_dask_client=False,
     return_dask_client=True,
     *args,
-    **kwargs
+    **kwargs,
 ):
     """
     This is not fully validated currently so may not work, please report bugs on the py4DSTEM github page.
@@ -225,7 +217,7 @@ def beta_parallel_disk_detection(
             probe_kernel_FT=dask_probe_delayed[0, 0],
             # probe_kernel_FT=delayed_probe_kernel_FT,
             *args,
-            **kwargs
+            **kwargs,
         )  # passing through args from earlier or should I use
         # corrPower=corrPower,
         # sigma=sigma_gaussianFilter,

py4DSTEM/braggvectors/threshold.py

@@ -26,7 +26,7 @@ def threshold_Braggpeaks(
             pattern
     """
     assert all(
-        [item in pointlistarray.dtype.fields for item in ["qx", "qy", "intensity"]]
+        item in pointlistarray.dtype.fields for item in ["qx", "qy", "intensity"]
     ), "pointlistarray must include the coordinates 'qx', 'qy', and 'intensity'."
     for Rx, Ry in tqdmnd(
         pointlistarray.shape[0],
@@ -113,7 +113,7 @@ def universal_threshold(
     assert isinstance(pointlistarray, PointListArray)
     assert metric in ("maximum", "average", "median", "manual")
     assert all(
-        [item in pointlistarray.dtype.fields for item in ["qx", "qy", "intensity"]]
+        item in pointlistarray.dtype.fields for item in ["qx", "qy", "intensity"]
     ), "pointlistarray must include the coordinates 'qx', 'qy', and 'intensity'."
     _pointlistarray = pointlistarray.copy()
     if name is None:

py4DSTEM/data/calibration.py

@@ -1,9 +1,7 @@
 # Defines the Calibration class, which stores calibration metadata
 
 import numpy as np
-from numbers import Number
 from typing import Optional
-from warnings import warn
 
 from emdfile import Metadata, Root
 from py4DSTEM.data.propagating_calibration import call_calibrate
@@ -505,7 +503,7 @@ def get_origin(self, rx=None, ry=None):
         qx0 = self._get_value("qx0", rx, ry)
         qy0 = self._get_value("qy0", rx, ry)
         ans = (qx0, qy0)
-        if any([x is None for x in ans]):
+        if any(x is None for x in ans):
             ans = None
         return ans
 
@@ -518,7 +516,7 @@ def get_origin_shift(self, rx=None, ry=None):
         qx0 = self._get_value("qx0_shift", rx, ry)
         qy0 = self._get_value("qy0_shift", rx, ry)
         ans = (qx0, qy0)
-        if any([x is None for x in ans]):
+        if any(x is None for x in ans):
             ans = None
         return ans
 
@@ -540,7 +538,7 @@ def get_origin_meas(self, rx=None, ry=None):
         qx0 = self._get_value("qx0_meas", rx, ry)
         qy0 = self._get_value("qy0_meas", rx, ry)
         ans = (qx0, qy0)
-        if any([x is None for x in ans]):
+        if any(x is None for x in ans):
             ans = None
         return ans
 
@@ -615,7 +613,7 @@ def get_ellipse(self, rx=None, ry=None):
         b = self.get_b(rx, ry)
         theta = self.get_theta(rx, ry)
         ans = (a, b, theta)
-        if any([x is None for x in ans]):
+        if any(x is None for x in ans):
             ans = None
         return ans
 
@@ -778,7 +776,7 @@ def get_probe_param(self):
         qx0 = self._get_value("qx0")
         qy0 = self._get_value("qy0")
         ans = (probe_semiangle, qx0, qy0)
-        if any([x is None for x in ans]):
+        if any(x is None for x in ans):
             ans = None
         return ans
 

py4DSTEM/datacube/datacube.py

@@ -12,7 +12,7 @@
 )
 from typing import Optional, Union
 
-from emdfile import Array, Metadata, Node, Root, tqdmnd
+from emdfile import Array, Metadata, Node, tqdmnd
 from py4DSTEM.data import Data, Calibration
 from py4DSTEM.datacube.virtualimage import DataCubeVirtualImager
 from py4DSTEM.datacube.virtualdiffraction import DataCubeVirtualDiffraction
@@ -653,7 +653,7 @@ def get_probe_size(
                 "dp_mean" in self.treekeys
             ), "calculate .get_dp_mean() or pass a `dp` arg"
             DP = self.tree("dp_mean").data
-        elif type(dp) == str:
+        elif isinstance(dp, str):
             assert dp in self.treekeys, f"mode {dp} not found in the tree"
             DP = self.tree(dp)
         elif type(dp) == np.ndarray:

py4DSTEM/datacube/virtualimage.py

@@ -414,7 +414,7 @@ def position_detector(
                 try:
                     image = self.tree(k)
                     break
-                except:
+                except AssertionError:
                     pass
             if image is None:
                 image = self[0, 0]

py4DSTEM/io/filereaders/read_K2.py

@@ -124,7 +124,8 @@ def __init__(
             # this may be wrong for binned data... in which case the reader doesn't work anyway!
             Q_Nx = gtg.allTags[".SI Image Tags.Acquisition.Parameters.Detector.height"]
             Q_Ny = gtg.allTags[".SI Image Tags.Acquisition.Parameters.Detector.width"]
-        except:
+        # TODO check this is the correct error type
+        except (ValueError, KeyError):
             print("Warning: diffraction pattern shape not detected!")
             print("Assuming 1920x1792 as the diffraction pattern size!")
             Q_Nx = 1792

py4DSTEM/io/filereaders/read_arina.py

@@ -1,5 +1,5 @@
 import h5py
-import hdf5plugin
+import hdf5plugin  # noqa: F401
 import numpy as np
 from py4DSTEM.datacube import DataCube
 from py4DSTEM.preprocess.utils import bin2D

py4DSTEM/io/filereaders/read_dm.py

@@ -1,7 +1,6 @@
 # Reads a digital micrograph 4D-STEM dataset
 
 import numpy as np
-from pathlib import Path
 from ncempy.io import dm
 from emdfile import tqdmnd, Array
 

py4DSTEM/io/filereaders/read_mib.py

@@ -14,7 +14,7 @@ def load_mib(
     reshape=True,
     flip=True,
     scan=(256, 256),
-    **kwargs
+    **kwargs,
 ):
     """
     Read a MIB file and return as py4DSTEM DataCube.