def validate(target_folder):
f = File(target_folder)
if len(File(target_folder).list(Filter())) > 0:
yn = YesNoCancelDialog(IJ.getInstance(), "Warning!", "Target folder is not empty! May overwrite files! Continue?")
if yn.yesPressed():
return True
else:
return False
return True
def save_etc(imp, info, output_folder):
"""handle saving output, final labelling and UI of what to do next"""
dialog = GenericDialog("Marksl1 cell shape prescreen");
dialog.addChoice("Vessel type: ",
info.get_vessel_types(),
info.get_vessel_type());
dialog.addStringField("Channel 1 label: ", info.get_ch1_label());
dialog.addStringField("Channel 2 label: ", info.get_ch2_label());
dialog.addStringField("Experiment identifier: ", info.get_experiment_id());
dialog.addStringField("Embryo identifier: ", info.get_embryo_id());
dialog.setOKLabel("Save preprocessing");
dialog.showDialog();
info.set_vessel_type(dialog.getNextChoice());
info.set_ch1_label(dialog.getNextString());
info.set_ch2_label(dialog.getNextString());
info.set_experiment_id(dialog.getNextString());
info.set_embryo_id(dialog.getNextString());
if dialog.wasCanceled():
return "stop";
if dialog.wasOKed():
exsting_files = os.listdir(output_folder);
r = re.compile(".*" + info.get_embryo_id() + " " + info.get_vessel_type() + ".*")
fns = filter(r.match, exsting_files)
numbers = list((int(s) for fn in fns for s in re.findall(r'\b\d+$', os.path.splitext(fn)[0])));
append_digit = (max(numbers) + 1) if numbers else 1;
ch1str = (info.get_ch1_label() + " ") if info.get_ch1_label() else "";
ch2str = (info.get_ch2_label() + " ") if info.get_ch2_label() else "";
expstr = (info.get_experiment_id() + " ") if info.get_experiment_id() else "";
file_name = ("Cropped " + ch1str + ch2str + expstr +
"e" + str(info.get_embryo_id()) + " " +
info.get_vessel_type() + " " +
str(append_digit));
FileSaver(imp).saveAsTiff(os.path.join(output_folder, (file_name + ".tif")));
info.save_info_to_json(os.path.join(output_folder, (file_name + ".json")));
continueDialog = YesNoCancelDialog(WM.getCurrentWindow(),
"Continue?",
"Continue with same input image or a new input image?",
"New image...",
"Same image");
if continueDialog.cancelPressed():
return "stop";
if continueDialog.yesPressed():
return "continue_newimage";
return "continue_sameimage";
return "stop";
#IL.wrap(img4D, "0-399").show()
showStack(img4D, title="%i-%i" % (first_timepoint, last_timepoint))
# Materialize (write to disk) the registered deconvolved stacks
targetDirN5 = os.path.join(targetDir, "deconvolved/n5/")
nameN5 = "%s_%i-%i_%ix%ix%ix%i" % (targetDir.split("/")[-2],
first_timepoint, last_timepoint,
img4D.dimension(0),
img4D.dimension(1),
img4D.dimension(2),
img4D.dimension(3))
writeN5Volume = True
if not os.path.exists(targetDirN5):
os.mkdir(targetDirN5)
else:
writeN5Volume = False
yn = YesNoCancelDialog(IJ.getInstance(), "Write N5",
"The N5 folder already exists: continue?")
writeN5Volume = yn.yesPressed()
if writeN5Volume:
print "N5 volume folder: ", targetDirN5
print "N5 volume name: ", nameN5
writeN5(img4D,
targetDirN5,
nameN5,
[img4D.dimension(0), img4D.dimension(1), 5, 1])
def check_fusion_settings(czi_path):
"""Check for fusion settings and asks confirmation to user if H5/XML fusion
Parameters
----------
czi_path : str
Path to the CZI file
Returns
-------
bool
Bool for fusion
str
Method of RAM handling
bool
Bool for TIFF or H5/XML fusion
"""
# Default values
do_fusion = True
fuse_tiff = True
reader = ZeissCZIReader()
m = DynamicMetadataOptions()
m.setBoolean(ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY, False)
m.setBoolean(ZeissCZIReader.RELATIVE_POSITIONS_KEY, True)
reader.setMetadataOptions(m)
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(str(czi_path))
nbr_tp = omeMeta.getTimestampAnnotationCount() + 1
nbr_chnl = omeMeta.getChannelCount(0)
# check the file size of the file to be fused and compare to the available RAM
# h5_filesize = os.path.getsize(export_path_temp + ".h5")
h5_filesize = os.path.getsize(czi_path) / 2
free_memory = get_free_memory()
print("h5 filesize " + convert_bytes(h5_filesize))
print("free memory in ij " + convert_bytes(free_memory))
# TODO: include in below calculation t_end, since only one t is fused at a time.
if free_memory > (6 * h5_filesize / downsampling):
ram_handling = "[Precompute Image]"
else:
ram_handling = "Virtual"
print("fusion mode used " + str(ram_handling))
# if autoselect_illuminations and nbr_ill > 1:
# ill_value = 2
# else:
# ill_value = 1
ram_requirement = 2 * h5_filesize / (nbr_tp * nbr_chnl * downsampling)
print(ram_requirement)
sufficient_ram = ram_requirement < free_memory / 10
if not sufficient_ram:
try:
yn = YesNoCancelDialog(
IJ.getInstance(),
"Warning!",
(
"File size is too big to use TIFF for fusion\n"
"Fusion will happen using H5/XML which might take weeks. Are you "
"sure you want to do fusion ?\n"
"All steps prior to fusion would still happen, allowing for manual "
"fusion and tile selection."
),
)
if yn.yesPressed():
fuse_tiff = False
else:
do_fusion = False
except Exception:
# when running headless the above will raise a java.awt.HeadlessException,
# so we simply fall back to the same behavior as if "No" was clicked:
do_fusion = False
return do_fusion, ram_handling, fuse_tiff