Merge pull request #286 from jonwright/master

Fixups

ImageD11/indexing.py

@@ -485,6 +485,7 @@ def assigntorings(self):
         )
         logging.info("Shape of scoring matrix", self.gvr.shape)
         self.gvflat = np.ascontiguousarray(self.gvr, float)  # Makes it contiguous
+        self.gv = np.ascontiguousarray(self.gv, float)
         # in memory, hkl fast index
 
     def friedelpairs(self, filename):

ImageD11/sinograms/lima_segmenter.py

@@ -25,6 +25,7 @@
 from ImageD11.sinograms import dataset
 import ImageD11.cImageD11
 
+
 try:
     from bslz4_to_sparse import chunk2sparse
 except ImportError:
@@ -434,6 +435,23 @@ def setup_slurm_array(dsname, dsgroup="/", pythonpath=None):
     logging.info("wrote " + sbat)
     return sbat
 
+def sbatchlocal(fname, cores=None):
+    """ 
+    Execute a grid batch job on the local machine
+    Loops over the array submission for you
+    """
+    import concurrent.futures
+    if cores is None:
+        cores = ImageD11.cImageD11.cores_available()
+    lines = open(fname,'r').readlines()
+    for line in lines:
+        if line.find('--array=')>=0:
+            start, end = line.split('=')[-1].split('-')
+    commands = [ 'SLURM_ARRAY_TASK_ID=%d bash %s > %s_%d.log'%(i, fname, fname, i )
+                for i in range(int(start), int(end)) ]
+    with concurrent.futures.ThreadPoolExecutor(max_workers = cores) as pool:
+        for _ in pool.map( os.system, commands ):
+            pass
 
 def setup(
     dsname,

ImageD11/sinograms/properties.py

@@ -955,13 +955,17 @@ def main(dsfilename, sparsefile=None, pksfile=None, options={}):
             options["nproc"] = max(1, nscans - 1)
         print("Nscans", nscans)
         print("Options", options)
-        peaks, ks, P, rmem = goforit(ds, sparsefile, options)  # ds.omega is passed here
-        t("%d label and pair" % (len(rmem.pk_props[0])))
-        if "save_overlaps" in options and options["save_overlaps"]:
-            rmem.save(pksfile + "_mat.h5", rc=True)
-            t("cache")
-        cc = rmem.find_uniq()
-        t("%s connected components" % (str(cc[0])))
+        if nscans > 1:
+            peaks, ks, P, rmem = goforit(ds, sparsefile, options)  # ds.omega is passed here
+            t("%d label and pair" % (len(rmem.pk_props[0])))
+            if "save_overlaps" in options and options["save_overlaps"]:
+                rmem.save(pksfile + "_mat.h5", rc=True)
+                t("cache")
+            cc = rmem.find_uniq()
+            t("%s connected components" % (str(cc[0])))
+        else:
+            # single scan. Skips a lot of hassle.
+            rmem = pks_table_from_scan(sparsefile, ds, 0)
         rmem.save(pksfile)
         t("write hdf5")
     except Exception as e:

ImageD11/sparseframe.py

@@ -258,6 +258,8 @@ def __init__( self, hname, scan, start = 0, n=None,
             for name in self.names:
                 if name in grp:
                     setattr( self, name, grp[name][s:e] )
+            if 'intensity' in self.names:
+                self.intensity = self.intensity.astype(np.float32)
             # pointers into this scan
             self.nnz = nnz[start:end]
             self.ipt = nnz_to_pointer( self.nnz )
@@ -327,7 +329,7 @@ def lmlabel(self, threshold = 0, countall=True, smooth=True  ):
         if smooth:
             self.signal = np.empty( self.intensity.shape, np.float32 )
         else:
-            self.signal = self.intensity
+            self.signal = self.intensity.astype(np.float32)
         # temporary workspaces
         npxmax = self.nnz.max()
         vmx = np.zeros( npxmax, np.float32 )

appveyor.yml

@@ -20,7 +20,7 @@ install:
   - "set TMPDIR=C:\\tmp"
   - python -c "import sys; print(sys.executable, sys.version)"
   - python -m pip install --upgrade pip setuptools
-  - python -m pip install pytest numpy
+  - python -m pip install pytest 'numpy<2'
   - python -m pip install --ignore-installed certifi --upgrade-strategy only-if-needed --only-binary=h5py --only-binary=scipy --only-binary=hdf5plugin .
 
 

pyproject.toml

@@ -3,5 +3,16 @@ requires = ["setuptools",
             "six",
             "wheel",
             "numpy; python_version=='2.7'",
+# There is no way to compile for versions < 1.25 and up to 2.
+# See https://numpy.org/doc/2.0/dev/depending_on_numpy.html
+#
+# This gives you all versions < 2.0
             "oldest-supported-numpy; python_version>='3.0'" ]
+#
+# This gives all versions > 1.25
+#            "numpy>=2.0.0rc1; python_version>='3.0'" ]
+#
+# As usual, the dependencies are not ready.
+# pin numpy < 2 for now.
+#
 build-backend = "setuptools.build_meta"

setup.py

@@ -142,7 +142,9 @@ def build_extension(self, ext):
 
 minimal = [  # can't compile without this
     "six",
-    "numpy",
+    'numpy ; python_version < "3"',
+    # Until the dependencies are ready
+    'numpy<2 ; python_version >= "3"',
     "setuptools",
     ]