fits2tmp 0.1.9__tar.gz → 0.2.0__tar.gz

{fits2tmp-0.1.9 → fits2tmp-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fits2tmp
-Version: 0.1.9
+Version: 0.2.0
 Summary: A way of loading FITS files into temporary filesystems to make them available in memory.
 Home-page: https://gitlab.developers.cam.ac.uk/phy/ra/vla22-phd/fits2tmp
 License: BSD-3-Clause

{fits2tmp-0.1.9 → fits2tmp-0.2.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fits2tmp"
-version = "0.1.9"
+version = "0.2.0"
 description = "A way of loading FITS files into temporary filesystems to make them available in memory."
 license = "BSD-3-Clause"
 authors = ["Verity Allan <vla22@cam.ac.uk>"]

{fits2tmp-0.1.9 → fits2tmp-0.2.0}/src/fits2tmp/fits2tmp.py

@@ -79,50 +79,64 @@ def fits2tmpfiles(inputpath, destination, chunks):
 
     return filepath
 
-def disk2fakefits(filetype, inputpath, destination, arraysize, chunks=None):
+def disk2fakefits(filetype, inputpath, destination, headerloc, arraysize, chunks=None):
+    # TODO: ADD code to handle arraysize differing from size of array in file
+    # maybe extend arr_size_check()?
+    destination = tempfile.TemporaryDirectory(dir=destination, delete=False)
     match filetype:
         case "fits":
             f = fits.open(inputpath)
-            d = da.from_array(f[0].data, chunks=chunks)
-            destination = tempfile.TemporaryDirectory(dir=destination, delete=False)
+            d = da.from_array(f[0].data[arraysize], chunks=chunks)
             n_header = dict2header(header_dict(f[0].header))
             wcs_obj = wcs.WCS(n_header)
         case "zarr":
-            bar
+            d = da.from_zarr(inputpath, chunks=chunks)[arraysize]
+            n_header = dict2header(file2dict(inputpath, headerloc))
+            wcs_obj = wcs.WCS(n_header)
         case "hdf5":
-            baz
+            f = h5py.File(filepath, "r")
+            #note this is hardcoded for the particular hdf5 files tested - needs parameterisation
+            d = da.from_array(f["array"][arraysize], chunks=chunks)
+            n_header = dict2header(file2dict(inputpath, headerloc))
+            wcs_obj = wcs.WCS(n_header)
+
         case "xradio":
             weeble
         case _:
             raise ValueError("The specified file type is not supported by fits2tmp.")
-    return d, destination, n_header, wcs_obj
-
-def fakefits2tmpfiles(filetype, inputpath, destination, arraysize, chunks=None):
-    darr, tempdest, n_header, wcs_obj = disk2fakefits(filetype, inputpath, destination, arraysize, chunks)
-    print(darr.shape)
+    return [d, destination, n_header, wcs_obj]
+
+def fakefits2tmpfiles(filetype, inputpath, destination, headerloc, arraysize, chunks=None):
+    inputarray = disk2fakefits(filetype, inputpath, destination, headerloc, arraysize, chunks)
+    darr = inputarray[0]
+    destination = inputarray[1]
+    header = inputarray[2]
+    wcs_obj = inputarray[3]
     dd = darr.to_delayed()
     fpaths = []
-    for i in range(dd.shape[0]):
+    for i in range(len(darr.chunks[0])):
         x = i * chunks[0] 
         x_delt = x + chunks[0] - 1
-        for j in range(dd.shape[1]):
+        for j in range(len(darr.chunks[1])):
+            print(i,j)
             y = j * chunks[1]
             y_delt = y + chunks[1] - 1
-            if len(dd.shape) == 2:
+            if len(darr.shape) == 2:
                 dest = str(i) + str(j)
                 data = dd[i][j]
                 wcs_coords = wcs_obj.slice((slice(x,x_delt), slice(y,y_delt)))
-            elif len(dd.shape) > 2:
-                for k in range(dd.shape[2]):
+            elif len(darr.shape) > 2:
+                for k in range(len(darr.chunks[2])):
+                    print(k)
                     data = dd[i][j][k]
                     z = k * chunks[2]
                     z_delt = z + chunks[2] - 1
-                    dest = str(i) + str(j) + str(k)
-                    t =wcs_obj[x:x_delt, y:y_delt, z:z_delt]
-                    n_header.update(t.to_header())
-                    hdu = fits.PrimaryHDU(data=data.compute(), header=n_header)
-                    hdu.writeto(tempdest.name + dest + "fits")
-                    fpaths.append(tempdest.name + dest + "fits")
+                    dest = '-' + str(i) +'-' + str(j) + '-' + str(k)
+                    t = wcs_obj[x:x_delt, y:y_delt, z:z_delt]
+                    header.update(t.to_header())
+                    hdu = fits.PrimaryHDU(data=data.compute(), header=header)
+                    hdu.writeto(destination.name + dest + "fits")
+                    fpaths.append(destination.name + dest + "fits")
     return fpaths
 #def array2disk(array, metadata, outputtype, destination):