def copy_plane(index, src):
p = J.call(planar_img, "getPlane", "(I)Ljava/lang/Object;", index)
dest = J.call(p, "getCurrentStorageArray", "()Ljava/lang/Object;")
length = np.prod(src.shape)
src = J.get_nice_arg(src, "[D")
J.static_call("java/lang/System", "arraycopy",
"(Ljava/lang/Object;ILjava/lang/Object;II)V",
src, 0, dest, 0, length)
def copy_plane(index, src):
p = J.call(planar_img, "getPlane", "(I)Ljava/lang/Object;", index)
dest = J.call(p, "getCurrentStorageArray", "()Ljava/lang/Object;")
length = np.prod(src.shape)
src = J.get_nice_arg(src, "[D")
J.static_call("java/lang/System", "arraycopy",
"(Ljava/lang/Object;ILjava/lang/Object;II)V", src, 0,
dest, 0, length)
def build_extractor(self):
'''Build a Java metadata extractor using the module settings'''
#
# Build a metadata extractor
#
script = """
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
extractor = new ImagePlaneMetadataExtractor();
extractor.addImagePlaneExtractor(new OMEMetadataExtractor());
extractor;
"""
extractor = J.run_script(script)
for group in self.extraction_methods:
if group.filter_choice == F_FILTERED_IMAGES:
fltr = J.make_instance(
"org/cellprofiler/imageset/filter/Filter",
"(Ljava/lang/String;)V", group.filter.value_text)
else:
fltr = None
if group.extraction_method == X_MANUAL_EXTRACTION:
if group.source == XM_FILE_NAME:
method = "addFileNameRegexp"
pattern = group.file_regexp.value
elif group.source == XM_FOLDER_NAME:
method = "addPathNameRegexp"
pattern = group.folder_regexp.value
J.call(extractor,
method,
"(Ljava/lang/String;Lorg/cellprofiler/imageset/filter/Filter;)V",
pattern, fltr)
elif group.extraction_method == X_IMPORTED_EXTRACTION:
#
# Create the array of key pairs for the join
#
key_pairs = []
for join_idx in group.csv_joiner.parse():
key_pair = J.make_instance(
'org/cellprofiler/imageset/ImportedMetadataExtractor$KeyPair',
'(Ljava/lang/String;Ljava/lang/String;)V',
join_idx[self.CSV_JOIN_NAME],
join_idx[self.IPD_JOIN_NAME])
key_pairs.append(key_pair)
key_pairs = J.get_nice_arg(
key_pairs,
"[Lorg/cellprofiler/imageset/ImportedMetadataExtractor$KeyPair;")
#
# Open the CSV file for reading, make an ImportedMetadataExtractor
# and install it in the big extractor
#
script = """
importPackage(Packages.org.cellprofiler.imageset);
var inputStream = new java.io.FileInputStream(csv_path);
var rdr = new java.io.InputStreamReader(inputStream);
var iextractor = new ImportedMetadataExtractor(rdr, key_pairs, case_insensitive);
extractor.addImagePlaneDetailsExtractor(iextractor, fltr);
"""
J.run_script(script, dict(
csv_path=group.csv_location.value,
key_pairs=key_pairs,
case_insensitive = group.wants_case_insensitive.value,
extractor = extractor,
fltr = fltr))
#
# Finally, we add the WellMetadataExtractor which has the inglorious
# job of making a well name from row and column, if present.
#
script = """
importPackage(Packages.org.cellprofiler.imageset);
extractor.addImagePlaneDetailsExtractor(new WellMetadataExtractor());
"""
J.run_script(script, dict(extractor = extractor))
return extractor
def build_extractor(self):
'''Build a Java metadata extractor using the module settings'''
#
# Build a metadata extractor
#
script = """
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
extractor = new ImagePlaneMetadataExtractor();
extractor.addImagePlaneExtractor(new OMEMetadataExtractor());
extractor;
"""
extractor = J.run_script(script)
for group in self.extraction_methods:
if group.filter_choice == F_FILTERED_IMAGES:
fltr = J.make_instance(
"org/cellprofiler/imageset/filter/Filter",
"(Ljava/lang/String;)V", group.filter.value_text)
else:
fltr = None
if group.extraction_method == X_MANUAL_EXTRACTION:
if group.source == XM_FILE_NAME:
method = "addFileNameRegexp"
pattern = group.file_regexp.value
elif group.source == XM_FOLDER_NAME:
method = "addPathNameRegexp"
pattern = group.folder_regexp.value
J.call(
extractor, method,
"(Ljava/lang/String;Lorg/cellprofiler/imageset/filter/Filter;)V",
pattern, fltr)
elif group.extraction_method == X_IMPORTED_EXTRACTION:
#
# Create the array of key pairs for the join
#
key_pairs = []
for join_idx in group.csv_joiner.parse():
key_pair = J.make_instance(
'org/cellprofiler/imageset/ImportedMetadataExtractor$KeyPair',
'(Ljava/lang/String;Ljava/lang/String;)V',
join_idx[self.CSV_JOIN_NAME],
join_idx[self.IPD_JOIN_NAME])
key_pairs.append(key_pair)
key_pairs = J.get_nice_arg(
key_pairs,
"[Lorg/cellprofiler/imageset/ImportedMetadataExtractor$KeyPair;"
)
#
# Open the CSV file for reading, make an ImportedMetadataExtractor
# and install it in the big extractor
#
script = """
importPackage(Packages.org.cellprofiler.imageset);
var inputStream = new java.io.FileInputStream(csv_path);
var rdr = new java.io.InputStreamReader(inputStream);
var iextractor = new ImportedMetadataExtractor(rdr, key_pairs, case_insensitive);
extractor.addImagePlaneDetailsExtractor(iextractor, fltr);
"""
J.run_script(
script,
dict(csv_path=group.csv_location.value,
key_pairs=key_pairs,
case_insensitive=group.wants_case_insensitive.value,
extractor=extractor,
fltr=fltr))
#
# Finally, we add the WellMetadataExtractor which has the inglorious
# job of making a well name from row and column, if present.
#
script = """
importPackage(Packages.org.cellprofiler.imageset);
extractor.addImagePlaneDetailsExtractor(new WellMetadataExtractor());
"""
J.run_script(script, dict(extractor=extractor))
return extractor