Release 0.10

.github/workflows/test.yml

@@ -51,7 +51,7 @@ jobs:
         miniforge-version: latest
     - name: Install ${{ matrix.conda-env }} dependencies
       run: |
-        sed -i 's/python/python=${{ matrix.python-version }}/' dependencies_${{ matrix.conda-env }}.yml
+        sed -i '/- python/d' dependencies_${{ matrix.conda-env }}.yml
         conda install -c conda-forge mpich
         conda env update --file dependencies_${{ matrix.conda-env }}.yml --name ptypy_env
         conda install -c conda-forge flake8 pytest pytest-cov

ptypy/core/illumination.py

@@ -409,7 +409,7 @@ def init_storage(storage, pars, energy=None, **kwargs):
             # Ok this is nearfield
             curve = 1.0
 
-        model = pod.bw(curve * np.sqrt(alldiff))
+        model = pod.bw(curve * np.sqrt(alldiff).astype(np.complex128))
     else:
         raise ValueError(
             prefix + 'Value to `model` key not understood in probe creation')

ptypy/experiment/hdf5_loader.py

@@ -320,6 +320,12 @@ class Hdf5Loader(PtyScan):
     type = list, ndarray
     help = This is the array or list with the re-ordered indices.
 
+    [nearfield_defocus]
+    default = None
+    type = float
+    help = Distance from sample to focus (for nearfield only)
+    doc = If set, magnification will be calculated automatically and applied to detector distance and pixelsize 
+
     """
 
     def __init__(self, pars=None, swmr=False, **kwargs):
@@ -378,6 +384,10 @@ def __init__(self, pars=None, swmr=False, **kwargs):
         if self.p.electron_data:
             self.meta.energy = u.m2keV(u.electron_wavelength(self.meta.energy))
 
+        # For nearfield data, manipulate distance and psize
+        if self.p.nearfield_defocus:
+            self._prepare_nearfield()
+
         # it's much better to have this logic here than in load!
         if (self._ismapped and (self._scantype == 'arb')):
             log(3, "This scan looks to be a mapped arbitrary trajectory scan.")
@@ -590,6 +600,20 @@ def _prepare_meta_info(self):
             assert self.pad.size == 4, "self.p.padding needs to of size 4"
             log(3, "Padding the detector frames by {}".format(self.p.padding))
 
+    def _prepare_nearfield(self):
+        """
+        Calculate magnification and modify distance and psize
+        """
+        defocus = self.p.nearfield_defocus
+        mag = self.meta.distance / defocus
+        dist_eff = (self.meta.distance - defocus) / mag
+        psize_eff = self.info.psize / mag
+        log(3, f"Nearfield: With defocus {defocus} m the magmification is {mag}")
+        log(3, f"Nearfield: The effective detector distance is {dist_eff}")
+        log(3, f"Nearfield: The effective pixel size is {psize_eff}")
+        self.meta.distance = dist_eff
+        self.info.psize = psize_eff
+
     def _prepare_center(self):
         """
         define how data should be loaded (center, cropping)

ptypy/utils/scripts.py

@@ -621,15 +621,15 @@ def stxm_analysis(storage, probe=None):
         pod = list(v.pods.values())[0]
         if not pod.active:
             continue
-        t = pod.diff.sum()
+        t = (pod.diff * pod.mask).sum()
         if t > t2:
             t2=t
         ss = v.slice
         # ss = (v.layer,
         #       slice(v.roi[0,0], v.roi[1,0]),
         #       slice(v.roi[0,1], v.roi[1,1]))
         # bufview = buf[ss]
-        m = mass_center(pod.diff) # + 1.
+        m = mass_center(pod.diff * pod.mask) # + 1.
         q = pod.di_view.storage._to_phys(m)
         dpc_row[ss] += q[0] * v.psize[0] * pr * 2 * np.pi / pod.geometry.lz
         dpc_col[ss] += q[1] * v.psize[1] * pr * 2 * np.pi / pod.geometry.lz
@@ -723,7 +723,7 @@ def phase_from_dpc(dpc_row, dpc_col):
 
     """
     py =- dpc_row
-    px =- dpc_col
+    px =+ dpc_col
     sh = px.shape
     sh = np.asarray(sh)
     fac = np.ones_like(sh)