misc tidy & import fixes

SIRF_data_preparation/evaluation_utilities.py

@@ -1,7 +1,7 @@
 """Some utilities for plotting objectives and metrics."""
 import csv
 from pathlib import Path
-from typing import Iterator
+from typing import Iterable, Iterator
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -19,7 +19,7 @@ def read_objectives(datadir='.'):
         return np.asarray([tuple(map(float, row)) for row in reader])
 
 
-def get_metrics(qm: QualityMetrics, iters: Iterator[int], srcdir='.'):
+def get_metrics(qm: QualityMetrics, iters: Iterable[int], srcdir='.'):
     """Read 'iter_{iter_glob}.hv' images from datadir, compute metrics and return as 2d array"""
     return np.asarray([
         list(qm.evaluate(STIR.ImageData(str(Path(srcdir) / f'iter_{i:04d}.hv'))).values()) for i in iters])
@@ -40,7 +40,7 @@ def pass_index(metrics: np.ndarray, thresh: Iterator, window: int = 1) -> int:
     return np.where(res)[0][0]
 
 
-def plot_metrics(iters: Iterator[int], m: np.ndarray, labels=None, suffix=""):
+def plot_metrics(iters: Iterable[int], m: np.ndarray, labels=None, suffix=""):
     """Make 2 subplots of metrics"""
     if labels is None:
         labels = [""] * m.shape[1]

SIRF_data_preparation/plot_BSREM_metrics.py

@@ -7,9 +7,10 @@
 import numpy
 
 import sirf.STIR as STIR
-import SIRF_data_preparation.data_QC as data_QC
 from petric import OUTDIR, SRCDIR, QualityMetrics, get_data
-from SIRF_data_preparation.evaluation_utilities import get_metrics, pass_index, plot_metrics, read_objectives
+
+from . import data_QC
+from .evaluation_utilities import get_metrics, pass_index, plot_metrics, read_objectives
 
 if not all((SRCDIR.is_dir(), OUTDIR.is_dir())):
     PETRICDIR = Path('~/devel/PETRIC').expanduser()

SIRF_data_preparation/prepare_mMR_NEMA_IQ_data.py

@@ -2,7 +2,7 @@
 import logging
 import os
 
-from data_utilities import prepare_challenge_Siemens_data, the_data_path
+from .data_utilities import prepare_challenge_Siemens_data, the_data_path
 
 this_directory = os.path.dirname(__file__)
 # sys.path.append(this_directory)

petric.py

@@ -20,7 +20,6 @@
 from dataclasses import dataclass
 from pathlib import Path
 from time import time
-from traceback import print_exc
 
 import numpy as np
 from skimage.metrics import mean_squared_error as mse
@@ -261,6 +260,8 @@ def get_image(fname):
         data = get_data(srcdir=srcdir, outdir=outdir)
         metrics[0].reset()
 else:
+    from traceback import print_exc
+
     from docopt import docopt
     args = docopt(__doc__)
     logging.basicConfig(level=getattr(logging, args["--log"].upper()))