Use Cython memoryviews in conversion to pandas

examples/find_peaks.py

@@ -12,4 +12,4 @@ print("Image shape:", arr.shape)
 peaks_tbl = find_peaks_single_panel(arr, os.path.join(THIS_DIR, '1panel.geom'))
 
 print(f"Found {len(peaks_tbl)} peaks")
-print(peaks_tbl.head())
+print(peaks_tbl)

pycrystfel/bindings.pyx

@@ -24,14 +24,11 @@ cdef featurelist_to_dataframe(crystfel.ImageFeatureList *flist):
     cdef:
         int i, nfeat = crystfel.image_feature_count(flist)
         crystfel.imagefeature *feat
-        cnp.ndarray[cnp.npy_double, ndim=1] ss, fs, rx, ry, rz, it
+        cnp.ndarray arr
+        double[:] ss, fs, rx, ry, rz, it
 
-    ss = np.zeros(nfeat, np.double)
-    fs = np.zeros(nfeat, np.double)
-    rx = np.zeros(nfeat, np.double)
-    ry = np.zeros(nfeat, np.double)
-    rz = np.zeros(nfeat, np.double)
-    it = np.zeros(nfeat, np.double)
+    arr = np.zeros((6, nfeat), dtype=np.double)
+    ss, fs, rx, ry, rz, it = arr
 
     with cython.boundscheck(False), cython.wraparound(False):
         for i in range(nfeat):
@@ -43,9 +40,9 @@ cdef featurelist_to_dataframe(crystfel.ImageFeatureList *flist):
             rz[i] = feat.rz
             it[i] = feat.intensity
 
-    return pd.DataFrame({
-        'ss': ss, 'fs': fs, 'rx': rx, 'ry': ry, 'rz': rz, 'intensity': it,
-    })
+    return pd.DataFrame(
+        arr.T, columns=['ss', 'fs', 'rx', 'ry', 'rz', 'intensity']
+    )
 
 
 
@@ -53,11 +50,9 @@ def find_peaks_single_panel(cnp.ndarray[cnp.npy_float, ndim=2] data, str geom_fi
     cdef:
         crystfel.beam_params beam
         crystfel.image image
-        void* bad_px_mask
 
     image.dp[0] = <float*>data.data
-    bad_px_mask = malloc(data.size * sizeof(int))
-    image.bad = <int**>&bad_px_mask
+    image.bad = NULL
     image.det = crystfel.get_detector_geometry(os.fsencode(geom_file), &beam)
     print(f"Loaded geometry with {image.det.n_panels} panels")
 
@@ -68,6 +63,7 @@ def find_peaks_single_panel(cnp.ndarray[cnp.npy_float, ndim=2] data, str geom_fi
         max_pix_count=200, local_bg_radius=3, min_res=0, max_res=1200,
         use_saturated=True,
     )
-    print("Done peak search")
+
+    crystfel.free_detector_geometry(image.det)
 
     return featurelist_to_dataframe(image.features)