Move get_detector_shape and pixels_to_image into detector.geom

src/geomtools/__init__.py

-# 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)

src/geomtools/detector/__init__.py

-# 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)

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

src/geomtools/sfx/__init__.py

-# 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

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

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