Compatibility with cfelpyutils 2.x & read/write bad regions from .geom file

.github/dependabot/constraints.txt

@@ -1,4 +1,4 @@
-cfelpyutils==1.0.1
+cfelpyutils==2.0.4
 cycler==0.10.0
 future==0.18.2
 h5py<3.5.0

extra_geom/base.py

@@ -1,7 +1,7 @@
 from itertools import chain
 
 import numpy as np
-from cfelpyutils.crystfel_utils import load_crystfel_geometry
+from cfelpyutils.geometry import load_crystfel_geometry
 
 from .crystfel_fmt import write_crystfel_geom
 from .snapped import GridGeometryFragment, SnappedGeometry
@@ -31,8 +31,8 @@ def from_panel_dict(cls, d):
         corner_pos = np.array([d['cnx']/res, d['cny']/res, d['coffset']])
         ss_vec = np.array([d['ssx'], d['ssy'], d['ssz']]) / res
         fs_vec = np.array([d['fsx'], d['fsy'], d['fsz']]) / res
-        ss_pixels = d['max_ss'] - d['min_ss'] + 1
-        fs_pixels = d['max_fs'] - d['min_fs'] + 1
+        ss_pixels = d['orig_max_ss'] - d['orig_min_ss'] + 1
+        fs_pixels = d['orig_max_fs'] - d['orig_min_fs'] + 1
         return cls(corner_pos, ss_vec, fs_vec, ss_pixels, fs_pixels)
 
     def corners(self):
@@ -244,15 +244,15 @@ def _cfel_panels_by_data_coord(cls, panels: dict):
             if len(ix_dims) > 1:
                 raise ValueError(f"Too many index dimensions for {pname}: {dims}")
 
-            min_ss = info['min_ss']
+            min_ss = info['orig_min_ss']
             if ix_dims:
                 # Geometry for 3D data, modules stacked along separate axis
                 modno = ix_dims[0]
             else:
                 # Geometry for 2D data, modules concatenated along slow-scan axis
                 modno, min_ss = divmod(min_ss, cls.expected_data_shape[1])
 
-            res[(modno, min_ss, info['min_fs'])] = info
+            res[(modno, min_ss, info['orig_min_fs'])] = info
 
         return res
 
@@ -262,8 +262,10 @@ def from_crystfel_geom(cls, filename):
 
         Returns a new geometry object.
         """
-        geom_dict = load_crystfel_geometry(filename)
-        panels_by_data_coord = cls._cfel_panels_by_data_coord(geom_dict['panels'])
+        cfel_geom = load_crystfel_geometry(filename)
+        panels_by_data_coord = cls._cfel_panels_by_data_coord(
+            cfel_geom.detector['panels']
+        )
         n_modules = cls.n_modules
         if n_modules == 0:
             # Detector type with varying number of modules (e.g. JUNGFRAU)
@@ -285,7 +287,7 @@ def from_crystfel_geom(cls, filename):
         cfel_md_keys = ('data', 'mask', 'adu_per_eV', 'clen')
         d1 = panels_by_data_coord[0, 0, 0]
         metadata = {'crystfel': {k: d1.get(k) for k in cfel_md_keys}}
-        # TODO: photon_energy (not returned with cfelpyutils 1.0)
+        metadata['crystfel']['photon_energy'] = cfel_geom.beam['photon_energy']
 
         return cls(modules, filename=filename, metadata=metadata)
 

extra_geom/tests/test_agipd500k2g_geometry.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 import xarray as xr
-from cfelpyutils.crystfel_utils import load_crystfel_geometry
+from cfelpyutils.geometry import load_crystfel_geometry
 from extra_data.stacking import stack_detector_data
 from matplotlib.axes import Axes
 
@@ -80,7 +80,7 @@ def test_write_read_crystfel_file(tmpdir):
     np.testing.assert_allclose(loaded.modules[0][0].fs_vec, geom.modules[0][0].fs_vec)
 
     # Load the geometry file with cfelpyutils and test the rigid groups
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
     quad_gr0 = [  # quadrant: p0a0 ... p7a7
         'p{}a{}'.format(p, a) for p, a in product(range(8), range(8))
     ]
@@ -89,10 +89,10 @@ def test_write_read_crystfel_file(tmpdir):
     assert geom_dict['rigid_groups']['q0'] == quad_gr0
     assert geom_dict['panels']['p0a0']['res'] == 5000  # 5000 pixels/metre
     p3a7 = geom_dict['panels']['p3a7']
-    assert p3a7['min_ss'] == 448
-    assert p3a7['max_ss'] == 511
-    assert p3a7['min_fs'] == 0
-    assert p3a7['max_fs'] == 127
+    assert p3a7['orig_min_ss'] == 448
+    assert p3a7['orig_max_ss'] == 511
+    assert p3a7['orig_min_fs'] == 0
+    assert p3a7['orig_max_fs'] == 127
 
 
 def test_write_read_crystfel_file_2d(tmpdir):
@@ -108,14 +108,14 @@ def test_write_read_crystfel_file_2d(tmpdir):
     np.testing.assert_allclose(loaded.modules[0][0].fs_vec, geom.modules[0][0].fs_vec)
 
     # Load the geometry file with cfelpyutils and check some values
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
 
     p3a7 = geom_dict['panels']['p3a7']
     assert p3a7['dim_structure'] == ['%', 'ss', 'fs']
-    assert p3a7['min_ss'] == (3 * 512) + 448
-    assert p3a7['max_ss'] == (3 * 512) + 511
-    assert p3a7['min_fs'] == 0
-    assert p3a7['max_fs'] == 127
+    assert p3a7['orig_min_ss'] == (3 * 512) + 448
+    assert p3a7['orig_max_ss'] == (3 * 512) + 511
+    assert p3a7['orig_min_fs'] == 0
+    assert p3a7['orig_max_fs'] == 127
 
 
 def test_inspect():

extra_geom/tests/test_agipd_geometry.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 import pytest
-from cfelpyutils.crystfel_utils import load_crystfel_geometry
+from cfelpyutils.geometry import load_crystfel_geometry
 from matplotlib.axes import Axes
 
 from extra_geom import AGIPD_1MGeometry, agipd_asic_seams
@@ -82,7 +82,7 @@ def test_write_read_crystfel_file(tmpdir):
     assert_geom_close(loaded, geom)
 
     # Load the geometry file with cfelpyutils and test the rigid groups
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
     quad_gr0 = [  # 1st quadrant: p0a0 ... p3a7
         'p{}a{}'.format(p, a) for p, a in product(range(4), range(8))
     ]
@@ -91,10 +91,10 @@ def test_write_read_crystfel_file(tmpdir):
     assert geom_dict['rigid_groups']['q0'] == quad_gr0
     assert geom_dict['panels']['p0a0']['res'] == 5000  # 5000 pixels/metre
     p3a7 = geom_dict['panels']['p3a7']
-    assert p3a7['min_ss'] == 448
-    assert p3a7['max_ss'] == 511
-    assert p3a7['min_fs'] == 0
-    assert p3a7['max_fs'] == 127
+    assert p3a7['orig_min_ss'] == 448
+    assert p3a7['orig_max_ss'] == 511
+    assert p3a7['orig_min_fs'] == 0
+    assert p3a7['orig_max_fs'] == 127
 
 
 def test_write_read_crystfel_file_2d(tmpdir):
@@ -112,14 +112,14 @@ def test_write_read_crystfel_file_2d(tmpdir):
     np.testing.assert_allclose(loaded.modules[0][0].fs_vec, geom.modules[0][0].fs_vec)
 
     # Load the geometry file with cfelpyutils and check some values
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
 
     p3a7 = geom_dict['panels']['p3a7']
     assert p3a7['dim_structure'] == ['%', 'ss', 'fs']
-    assert p3a7['min_ss'] == (3 * 512) + 448
-    assert p3a7['max_ss'] == (3 * 512) + 511
-    assert p3a7['min_fs'] == 0
-    assert p3a7['max_fs'] == 127
+    assert p3a7['orig_min_ss'] == (3 * 512) + 448
+    assert p3a7['orig_max_ss'] == (3 * 512) + 511
+    assert p3a7['orig_min_fs'] == 0
+    assert p3a7['orig_max_fs'] == 127
 
 
 def test_quad_positions():

extra_geom/tests/test_epix_geometry.py

@@ -1,7 +1,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
-from cfelpyutils.crystfel_utils import load_crystfel_geometry
+from cfelpyutils.geometry import load_crystfel_geometry
 
 import extra_geom
 from extra_geom import Epix10KGeometry, Epix100Geometry
@@ -132,14 +132,14 @@ def test_write_read_crystfel_file(args, tmpdir):
     assert_geom_close(loaded, epix)
 
     # Load the geometry file with cfelpyutils and test the rigid groups
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
     assert geom_dict['panels']['p0a0']['res'] == 1 / pxsz
     assert len(geom_dict['panels']) == 4
     p0a0 = geom_dict['panels']['p0a0']
-    assert p0a0['max_ss'] == nrow - 1
-    assert p0a0['min_ss'] == 0
-    assert p0a0['max_fs'] == ncol - 1
-    assert p0a0['min_fs'] == 0
+    assert p0a0['orig_max_ss'] == nrow - 1
+    assert p0a0['orig_min_ss'] == 0
+    assert p0a0['orig_max_fs'] == ncol - 1
+    assert p0a0['orig_min_fs'] == 0
 
 
 @pytest.mark.parametrize('args', ['epix100'], indirect=True)

extra_geom/tests/test_jungfrau_geometry.py

@@ -1,6 +1,6 @@
 
 import numpy as np
-from cfelpyutils.crystfel_utils import load_crystfel_geometry
+from cfelpyutils.geometry import load_crystfel_geometry
 
 from extra_geom import JUNGFRAUGeometry
 
@@ -33,15 +33,16 @@ def test_write_read_crystfel_file(tmpdir):
     assert_geom_close(loaded, geom)
     assert loaded.metadata['crystfel']['adu_per_eV'] == 0.0042
     assert loaded.metadata['crystfel']['clen'] == 0.101
+    assert loaded.metadata['crystfel']['photon_energy'] == 9000
 
     # Load the geometry file with cfelpyutils and test the rigid groups
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
     assert geom_dict['panels']['p0a0']['res'] == 1 / 75e-6
     p3a7 = geom_dict['panels']['p3a7']
-    assert p3a7['min_ss'] == 256
-    assert p3a7['max_ss'] == 511
-    assert p3a7['min_fs'] == 768
-    assert p3a7['max_fs'] == 1023
+    assert p3a7['orig_min_ss'] == 256
+    assert p3a7['orig_max_ss'] == 511
+    assert p3a7['orig_min_fs'] == 768
+    assert p3a7['orig_max_fs'] == 1023
 
     # Check that metadata is written back to .geom file OK
     path2 = str(tmpdir / 'test2.geom')

extra_geom/tests/test_lpd_geometry.py

@@ -4,7 +4,7 @@
 import h5py
 import numpy as np
 import pytest
-from cfelpyutils.crystfel_utils import load_crystfel_geometry
+from cfelpyutils.geometry import load_crystfel_geometry
 from matplotlib.axes import Axes
 from testpath import assert_isfile
 
@@ -38,7 +38,7 @@ def test_write_read_crystfel_file(tmpdir):
     np.testing.assert_allclose(loaded.modules[0][0].fs_vec, geom.modules[0][0].fs_vec)
 
 
-    geom_dict = load_crystfel_geometry(path)
+    geom_dict = load_crystfel_geometry(path).detector
     quad_gr0 = ['p0a0', 'p0a1', 'p0a2', 'p0a3', 'p0a4', 'p0a5', 'p0a6', 'p0a7',
                 'p0a8', 'p0a9', 'p0a10','p0a11', 'p0a12', 'p0a13', 'p0a14',
                 'p0a15', 'p1a0', 'p1a1','p1a2', 'p1a3','p1a4','p1a5','p1a6',

setup.py

@@ -37,7 +37,7 @@ def find_version(*parts):
           'extra_geom.tests': ['dssc_geo_june19.h5', 'lpd_mar_18.h5'],
       },
       install_requires=[
-          'cfelpyutils>=0.92, <2.0',
+          'cfelpyutils>=2.0, <3.0',
           'h5py>=2.7.1',
           'matplotlib',
           'numpy',