From 85ade0292481e2c3b51efe253f9bf10a53316cdc Mon Sep 17 00:00:00 2001
From: Egor Sobolev <egor.sobolev@xfel.eu>
Date: Mon, 22 Jul 2024 17:00:45 +0200
Subject: [PATCH] Move get_detector_shape and pixels_to_image into
detector.geom
---
src/geomtools/__init__.py | 22 ++++++++++------------
src/geomtools/detector/__init__.py | 8 ++++----
src/geomtools/detector/geom.py | 20 ++++++++++++++++++++
src/geomtools/sfx/__init__.py | 26 ++++++++++++++------------
src/geomtools/sfx/misc.py | 20 --------------------
src/geomtools/sfx/optimiser.py | 6 ++++--
6 files changed, 52 insertions(+), 50 deletions(-)
diff --git a/src/geomtools/__init__.py b/src/geomtools/__init__.py
index 9bfac93..3f182b0 100644
--- a/src/geomtools/__init__.py
+++ b/src/geomtools/__init__.py
@@ -1,12 +1,10 @@
-# flake8: noqa E401
-from .detector import (assemble_data, get_pixel_positions,
- plot_data_on_detector, plot_detector_layout,
- read_crystfel_geom, write_crystfel_geom)
-from .sfx import (avg_pixel_displacement, badpixels_mask, cell_volume, ellipse,
- extract_cell, extract_geometry, gauss2d_fit,
- get_min_bragg_dist, get_peak_position, get_q_from_xyz,
- parse_crystfel_streamfile, parse_xwiz_summary,
- ph_en_to_lambda, pixels_to_image, plot_cell_parameters,
- plot_center_shift, plot_geoptimiser_errormap, plot_peakogram,
- plot_powder, read_crystfel_cell, read_crystfel_streamfile,
- refine_geometry, rmsd_per_group, spacing)
+from .detector import ( # noqa E401
+ assemble_data, get_pixel_positions, pixels_to_image, plot_data_on_detector,
+ plot_detector_layout, read_crystfel_geom, write_crystfel_geom)
+from .sfx import ( # noqa E401
+ avg_pixel_displacement, badpixels_mask, cell_volume, ellipse, extract_cell,
+ extract_geometry, gauss2d_fit, get_min_bragg_dist, get_peak_position,
+ get_q_from_xyz, parse_crystfel_streamfile, parse_xwiz_summary,
+ ph_en_to_lambda, plot_cell_parameters, plot_center_shift,
+ plot_geoptimiser_errormap, plot_peakogram, plot_powder, read_crystfel_cell,
+ read_crystfel_streamfile, refine_geometry, rmsd_per_group, spacing)
diff --git a/src/geomtools/detector/__init__.py b/src/geomtools/detector/__init__.py
index bfc3892..e6f2a82 100644
--- a/src/geomtools/detector/__init__.py
+++ b/src/geomtools/detector/__init__.py
@@ -1,4 +1,4 @@
-# flake8: noqa E401
-from .crystfel_frm import read_crystfel_geom, write_crystfel_geom
-from .geom import get_pixel_positions, assemble_data
-from .draw import plot_detector_layout, plot_data_on_detector
+from .crystfel_frm import read_crystfel_geom, write_crystfel_geom # noqa E401
+from .draw import plot_data_on_detector, plot_detector_layout # noqa E401
+from .geom import ( # noqa E401
+ assemble_data, get_detector_shape, get_pixel_positions, pixels_to_image)
diff --git a/src/geomtools/detector/geom.py b/src/geomtools/detector/geom.py
index e55e78a..b8b11de 100644
--- a/src/geomtools/detector/geom.py
+++ b/src/geomtools/detector/geom.py
@@ -55,3 +55,23 @@ def assemble_data(data, pos):
img[y - ymin, x - xmin] = data
return img, (-xmin, -ymin)
+
+
+def get_detector_shape(panels):
+ """Returns the shape of detector image array."""
+ ixmax = (
+ panels[['modno', 'orig_max_ss', 'orig_max_fs']].max()
+ .rename({'orig_max_fs': 'fs', 'orig_max_ss': 'ss'})
+ )
+ ixmin = (
+ panels[['modno', 'orig_min_ss', 'orig_min_fs']].min()
+ .rename({'orig_min_fs': 'fs', 'orig_min_ss': 'ss'})
+ )
+ return tuple((ixmax - ixmin + 1).tolist())
+
+
+def pixels_to_image(shape, px, attr='msk'):
+ """Transforms dataset of pixels to the image array."""
+ img = np.zeros(shape, px[attr].dtype)
+ img[px.modno, px.ss, px.fs] = px[attr]
+ return img
diff --git a/src/geomtools/sfx/__init__.py b/src/geomtools/sfx/__init__.py
index a9c1675..c00fdfe 100644
--- a/src/geomtools/sfx/__init__.py
+++ b/src/geomtools/sfx/__init__.py
@@ -1,12 +1,14 @@
-# flake8: noqa E401
-from .crystfelio import (extract_cell, extract_geometry,
- parse_crystfel_streamfile, read_crystfel_streamfile)
-from .draw import (plot_cell_parameters, plot_center_shift,
- plot_geoptimiser_errormap, plot_peakogram, plot_powder)
-from .lattice import (cell_volume, get_min_bragg_dist, get_q_from_xyz,
- ph_en_to_lambda, read_crystfel_cell, spacing)
-from .misc import (avg_pixel_displacement, badpixels_mask, ellipse,
- gauss2d_fit, get_detector_shape, get_peak_position,
- pixels_to_image, rmsd_per_group)
-from .refine import refine_geometry
-from .xwizio import parse_xwiz_summary
+from .crystfelio import ( # noqa E401
+ extract_cell, extract_geometry, parse_crystfel_streamfile,
+ read_crystfel_streamfile)
+from .draw import ( # noqa E401
+ plot_cell_parameters, plot_center_shift, plot_geoptimiser_errormap,
+ plot_peakogram, plot_powder)
+from .lattice import ( # noqa E401
+ cell_volume, get_min_bragg_dist, get_q_from_xyz, ph_en_to_lambda,
+ read_crystfel_cell, spacing)
+from .misc import ( # noqa E401
+ avg_pixel_displacement, badpixels_mask, ellipse, gauss2d_fit,
+ get_peak_position, rmsd_per_group)
+from .refine import refine_geometry # noqa E401
+from .xwizio import parse_xwiz_summary # noqa E401
diff --git a/src/geomtools/sfx/misc.py b/src/geomtools/sfx/misc.py
index e3ef0a6..927d099 100644
--- a/src/geomtools/sfx/misc.py
+++ b/src/geomtools/sfx/misc.py
@@ -116,23 +116,3 @@ def badpixels_mask(pe, panels, snr=6, min_peak_count=4):
px = px.join(rp, on="ri")
px['msk'] = (px.num_peaks > px.num_peaks_hi)
return px
-
-
-def get_detector_shape(panels):
- """Returns the shape of detector image array."""
- ixmax = (
- panels[['modno', 'orig_max_ss', 'orig_max_fs']].max()
- .rename({'orig_max_fs': 'fs', 'orig_max_ss': 'ss'})
- )
- ixmin = (
- panels[['modno', 'orig_min_ss', 'orig_min_fs']].min()
- .rename({'orig_min_fs': 'fs', 'orig_min_ss': 'ss'})
- )
- return tuple((ixmax - ixmin + 1).tolist())
-
-
-def pixels_to_image(shape, px, attr='msk'):
- """Transforms dataset of pixels to the image array."""
- img = np.zeros(shape, px[attr].dtype)
- img[px.modno, px.ss, px.fs] = px[attr]
- return img
diff --git a/src/geomtools/sfx/optimiser.py b/src/geomtools/sfx/optimiser.py
index 3bf6d23..391e8cc 100644
--- a/src/geomtools/sfx/optimiser.py
+++ b/src/geomtools/sfx/optimiser.py
@@ -4,9 +4,11 @@ import tempfile
import h5py
-from ..detector import read_crystfel_geom, write_crystfel_geom
+from ..detector import (
+ get_detector_shape, pixels_to_image, read_crystfel_geom,
+ write_crystfel_geom)
from .crystfelio import extract_geometry, read_crystfel_streamfile
-from .misc import badpixels_mask, get_detector_shape, pixels_to_image
+from .misc import badpixels_mask
from .refine import refine_geometry
--
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