Changes for API in CrystFEL master branch

pycrystfel/bindings.pyx

@@ -16,65 +16,69 @@ def progress_bar(val, total, text):
 
 
 def inspect_geom_file(path):
-    cdef crystfel.detector *det
-    cdef crystfel.beam_params beam
-    det = crystfel.get_detector_geometry(os.fsencode(path), &beam)
-    print("n_panels:", det.n_panels)
-    print("panel names:", [det.panels[i].name for i in range(det.n_panels)])
-    print("photon energy:", beam.photon_energy)
-    crystfel.free_detector_geometry(det)
+    cdef:
+        crystfel.DataTemplate* dt
+        crystfel.image* img
+    dt = crystfel.data_template_new_from_file(os.fsencode(path))
+    img = crystfel.image_create_for_simulation(dt)
+    crystfel.data_template_free(dt)
+
+    print("n_panels:", img.detgeom.n_panels)
+    print("panel names:", [
+        img.detgeom.panels[i].name for i in range(img.detgeom.n_panels)
+    ])
+    crystfel.image_free(img)
 
 cdef featurelist_to_dataframe(crystfel.ImageFeatureList *flist):
     cdef:
         int i, nfeat = crystfel.image_feature_count(flist)
         crystfel.imagefeature *feat
         cnp.ndarray arr
-        double[:] ss, fs, rx, ry, rz, it
+        double[:] ss, fs, it
 
-    arr = np.zeros((6, nfeat), dtype=np.double)
-    ss, fs, rx, ry, rz, it = arr
+    arr = np.zeros((3, nfeat), dtype=np.double)
+    ss, fs, it = arr
 
     with cython.boundscheck(False), cython.wraparound(False):
         for i in range(nfeat):
             feat = crystfel.image_get_feature(flist, i)
             ss[i] = feat.ss
             fs[i] = feat.fs
-            rx[i] = feat.rx
-            ry[i] = feat.ry
-            rz[i] = feat.rz
             it[i] = feat.intensity
 
     return pd.DataFrame(
-        arr.T, columns=['ss', 'fs', 'rx', 'ry', 'rz', 'intensity']
+        arr.T, columns=['ss', 'fs', 'intensity']
     )
 
 def find_peaks_single_panel(cnp.ndarray[cnp.npy_float, ndim=2] data, str geom_file):
     cdef:
+        crystfel.DataTemplate* dt
         crystfel.beam_params beam
-        crystfel.image image
+        crystfel.image* image
 
-    image.dp[0] = <float*>data.data
-    image.bad = NULL
-    image.det = crystfel.get_detector_geometry(os.fsencode(geom_file), &beam)
-    print(f"Loaded geometry with {image.det.n_panels} panels")
+    dt = crystfel.data_template_new_from_file(os.fsencode(geom_file))
+    image = crystfel.image_create_for_simulation(dt)
+    crystfel.data_template_free(dt)
 
-    image.features = NULL
+    free(image.dp[0])
+    image.dp[0] = <float*>data.data
+    print(f"Loaded geometry with {image.detgeom.n_panels} panels")
 
     crystfel.search_peaks_peakfinder8(
-        &image, max_n_peaks=200, threshold=20, min_snr=3, min_pix_count=2,
+        image, max_n_peaks=200, threshold=20, min_snr=3, min_pix_count=2,
         max_pix_count=200, local_bg_radius=3, min_res=0, max_res=1200,
         use_saturated=True,
     )
 
-    crystfel.free_detector_geometry(image.det)
+    df = featurelist_to_dataframe(image.features)
 
-    return featurelist_to_dataframe(image.features)
+    crystfel.image_free(image)
 
 
 # Pointer wrapper machinery based on Cython docs:
 # https://cython.readthedocs.io/en/latest/src/userguide/extension_types.html#instantiation-from-existing-c-c-pointers
 cdef class Detector:
-    cdef crystfel.detector* _ptr
+    cdef crystfel.image* _img
     cdef bint ptr_owner
 
     def __cinit__(self):
@@ -82,27 +86,29 @@ cdef class Detector:
 
     def __dealloc__(self):
         # De-allocate if not null and flag is set
-        if self._ptr is not NULL and self.ptr_owner is True:
-            free(self._ptr)
-            self._ptr = NULL
+        if self._img is not NULL and self.ptr_owner is True:
+            crystfel.image_free(self._img)
+            self._img = NULL
 
     @staticmethod
-    cdef Detector from_ptr(crystfel.detector* _ptr, bint owner=False):
+    cdef Detector from_image_ptr(crystfel.image* _img, bint owner=False):
         # Call to __new__ bypasses __init__ constructor
         cdef Detector det = Detector.__new__(Detector)
-        det._ptr = _ptr
+        det._img = _img
         det.ptr_owner = owner
         return det
 
     @classmethod
     def from_filename(cls, path):
-        return Detector.from_ptr(
-            crystfel.get_detector_geometry(os.fsencode(path), NULL), owner=True
-        )
+        cdef crystfel.DataTemplate* dt = \
+            crystfel.data_template_new_from_file(os.fsencode(path))
+        cdef crystfel.image* img = crystfel.image_create_for_simulation(dt)
+        crystfel.data_template_free(dt)
+        return Detector.from_image_ptr(img)
 
     @property
     def n_panels(self):
-        return self._ptr.n_panels if self._ptr is not NULL else 0
+        return self._img.detgeom.n_panels if self._img is not NULL else 0
 
     def panel_names(self):
-        return [self._ptr.panels[i].name.decode('utf-8') for i in range(self.n_panels)]
+        return [self._img.detgeom.panels[i].name.decode('utf-8') for i in range(self.n_panels)]

pycrystfel/crystfel.pxd

@@ -30,20 +30,27 @@ cdef extern from "crystfel/index.h":
     INDEXING_USE_LATTICE_TYPE,
     INDEXING_USE_CELL_PARAMETERS
 
-cdef extern from "crystfel/detector.h":
-  cdef struct panel:
-    char name[1024]
-    double coffset
-    double clen
+cdef extern from "crystfel/detgeom.h":
+  cdef struct detgeom_panel:
+    char* name
+    double cnx
+    double cny
+    double cnz
     # ...
 
-  cdef struct detector:
-    panel *panels
+  cdef struct detgeom:
+    detgeom_panel* panels
     int n_panels
-    # ...
 
-  detector* get_detector_geometry(const char *filename, beam_params *beam)
-  void free_detector_geometry(detector *det)
+  void detgeom_free(detgeom* det)
+
+cdef extern from "crystfel/datatemplate.h":
+  ctypedef struct DataTemplate:
+    pass   # Opaque struct, used through functions
+
+  DataTemplate *data_template_new_from_file(const char* filename)
+  DataTemplate *data_template_new_from_string(const char* string_in)
+  void data_template_free(DataTemplate* dt)
 
 cdef extern from "crystfel/spectrum.h":
   ctypedef struct Spectrum:
@@ -57,29 +64,25 @@ cdef extern from "crystfel/image.h":
     double bandwidth
 
   cdef struct imagefeature:  # description of a peak
-    image *parent
-    panel *p
+    int pn  # Panel number
     double intensity
     const char *name
     double fs   # Fast-scan & slow-scan coordinates, pixels from panel corner
     double ss
-    double rx   # Reciprocal space coordinates (m^-1)
-    double ry
-    double rz
 
   ctypedef struct ImageFeatureList:
     pass  # Opaque struct, used through functions
 
   ImageFeatureList* image_feature_list_new()
-  void image_feature_list_free(ImageFeatureList *flist)
+  void image_feature_list_free(ImageFeatureList* flist)
   void image_add_feature(
-      ImageFeatureList *flist, double x, double y, panel *p, image *parent,
-      double intensity, const char *name
+      ImageFeatureList* flist, double x, double y, int pn, image* parent,
+      double intensity, const char* name
   )
   imagefeature* image_get_feature(ImageFeatureList *flist, int idx)
   void image_remove_feature(ImageFeatureList *flist, int idx)
   imagefeature* image_feature_closest(
-      ImageFeatureList *flist, double fs, double ss, panel *p, double *d, int *idx
+      ImageFeatureList* flist, double fs, double ss, int pn, double* d, int* idx
   )
   int image_feature_count(ImageFeatureList *flist)
 
@@ -94,18 +97,22 @@ cdef extern from "crystfel/image.h":
     int n_crystals
     IndexingMethod indexed_by
     int n_indexing_tries
-    detector *det
-    beam_params *beam
+    detgeom* detgeom
+    char* filename
+    char* ev  # Event ID
     double avg_clen
     int id
     int serial
     Spectrum* spectrum
-    double lambda_ "lambda"
-    double div
-    double bw
-    double peak_resolution
-    ImageFeatureList *features
-    char* filename
+    double lambda_ "lambda"  # Wavelength of the incident radiation, in metres
+    double div  # Convergence angle of the incident ration, in radians (full angle)
+    double bw  # Full-width half-maximum bandwidth as a fraction, applied to wavelength
+    double peak_resolution  # Resolution estimate based on peaks
+    ImageFeatureList* features
+
+  image* image_new()
+  void image_free(image* image)
+  image* image_create_for_simulation(const DataTemplate* dtempl)
 
 cdef extern from "crystfel/peaks.h":
   int search_peaks_peakfinder8(