From 78547b5ad423c194b056df813b4bf9f92a068ece Mon Sep 17 00:00:00 2001
From: Florian Lauck <florian.lauck@cfel.de>
Date: Wed, 22 Sep 2021 16:42:15 +0200
Subject: [PATCH] Fix return type in peakfinder
---
cfelpyutils/peakfinding/peakfinder8.py | 51 ++++++++++++++++----------
tests/peakfinding/test_peakfinder8.py | 10 ++---
2 files changed, 36 insertions(+), 25 deletions(-)
diff --git a/cfelpyutils/peakfinding/peakfinder8.py b/cfelpyutils/peakfinding/peakfinder8.py
index 6a32ab6..8d80fad 100644
--- a/cfelpyutils/peakfinding/peakfinder8.py
+++ b/cfelpyutils/peakfinding/peakfinder8.py
@@ -18,20 +18,31 @@ Peakfinder8 algorithm for detection of Bragg peaks in detector frame data.
"""
import sys
-from typing import Type, List, Union
+from collections import namedtuple
+from typing import Union
import h5py # type: ignore
import numpy # type: ignore
-from mypy_extensions import TypedDict
from .lib import peakfinder_8
+PeakList = namedtuple("PeakList", ["num_peaks", "fs", "ss", "intensity"])
+"""
+Information about Bragg peaks found in a detector data frame (list of peaks).
+
+Arguments:
-TypePeakList = TypedDict(
- "TypePeakList",
- {"num_peaks": int, "fs": List[float], "ss": List[float], "intensity": List[float]},
- total=True,
-)
+ num_peaks(int): number of peaks that were detected in the data frame.
+
+ fs (List[float]): a list of fractional fs indexes locating the detected peaks
+ in the detector data frame.
+
+ ss (List[float]): a list of fractional ss indexes locating the detected peaks
+ in the detector data frame.
+
+ intensity (List[float]): a list of integrated intensities for the detected
+ peaks.
+"""
class Peakfinder8PeakDetection:
@@ -167,7 +178,7 @@ class Peakfinder8PeakDetection:
else:
self._mask = None
- def find_peaks(self, data: numpy.ndarray) -> TypePeakList:
+ def find_peaks(self, data: numpy.ndarray) -> PeakList:
"""
Finds peaks in a detector data frame.
@@ -181,19 +192,19 @@ class Peakfinder8PeakDetection:
Returns:
- TypePeakList: a dictionary with information about the Bragg peaks
- detected in a data frame. The dictionary has the following keys:
+ PeakList: a namedtuple with information about the Bragg peaks
+ detected in a data frame. The object has the following attributes:
- - A key named "num_peaks" whose value is the number of peaks that were
+ - An attribute named "num_peaks" whose value is the number of peaks that were
detected in the data frame.
- - A key named 'fs' whose value is a list of fractional fs indexes locating
+ - An attribute named 'fs' whose value is a list of fractional fs indexes locating
the detected peaks in the data frame.
- - A key named 'ss' whose value is a list of fractional ss indexes locating
+ - An attribute named 'ss' whose value is a list of fractional ss indexes locating
the detected peaks in the data frame.
- - A key named 'intensity' whose value is a list of integrated intensities
+ - An attribute named 'intensity' whose value is a list of integrated intensities
for the detected peaks.
"""
if not self._mask_initialized:
@@ -223,9 +234,9 @@ class Peakfinder8PeakDetection:
self._local_bg_radius,
)
- return {
- "num_peaks": len(peak_list[0]),
- "fs": peak_list[0],
- "ss": peak_list[1],
- "intensity": peak_list[2],
- }
+ return PeakList(
+ num_peaks=len(peak_list[0]),
+ fs=peak_list[0],
+ ss=peak_list[1],
+ intensity=peak_list[2],
+ )
diff --git a/tests/peakfinding/test_peakfinder8.py b/tests/peakfinding/test_peakfinder8.py
index 49d5fac..9a95bd6 100644
--- a/tests/peakfinding/test_peakfinder8.py
+++ b/tests/peakfinding/test_peakfinder8.py
@@ -16,7 +16,7 @@
import numpy
import pytest
-from cfelpyutils.geometry import compute_pix_maps, load_crystfel_geometry
+from cfelpyutils.geometry import compute_pix_maps
from cfelpyutils.peakfinding.peakfinder8 import Peakfinder8PeakDetection
from tests.fixtures import detector_geometry
@@ -82,7 +82,7 @@ class TestPeakfinder8PeakDetection:
def test_find_peak(self, peakfinder_config, detector_image_with_4_peaks):
peakfinder = Peakfinder8PeakDetection(**peakfinder_config)
peak_list = peakfinder.find_peaks(detector_image_with_4_peaks)
- assert peak_list["num_peaks"] == 4
- assert len(peak_list["intensity"]) == 4
- assert len(peak_list["fs"]) == 4
- assert len(peak_list["ss"]) == 4
+ assert peak_list.num_peaks == 4
+ assert len(peak_list.intensity) == 4
+ assert len(peak_list.fs) == 4
+ assert len(peak_list.ss) == 4
--
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