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Fixed import issue that prevented use of script with default FIJI installation #3

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Fixed import issue that prevented use of script with default FIJI installation #3

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57d5f23
added try-except block for KLB import
mwinding Dec 16, 2020
94b0819
minor whitespace change
mwinding Dec 16, 2020
c1e2131
minor whitespace change
mwinding Dec 16, 2020
007cbc2
minor whitespace change
mwinding Dec 16, 2020
ac937de
minor whitespace change
mwinding Dec 16, 2020
7c5bf1a
updated the default paths for mac
mwinding Dec 16, 2020
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14 changes: 11 additions & 3 deletions python/imagej/tabulate_filepaths.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,13 @@
import re
import os
import sys
from org.janelia.simview.klb import KLB

try: # try-except block allows users with default FIJI to run the script without KLB installation
from org.janelia.simview.klb import KLB
except ImportError:
print "Warning: KLB format unavailable"
KLB = None

from net.imglib2.img.display.imagej import ImageJFunctions as IL


Expand All @@ -35,8 +41,8 @@
base_path = None

# Laptop via sshfs
#txt_file = "/home/albert/zstore1/barnesc/LarvalScreen.txt"
#base_path = "/home/albert/zstore1/barnesc/flylight-backups/LarvalScreen/"
txt_file = "/Volumes/zfs/barnesc/flylight-backups/LarvalScreen/manifest.txt"
base_path = "/Volumes/zfs/barnesc/flylight-backups/LarvalScreen/"

# At LMB desktop:
#txt_file = "/home/albert/LarvalScreen.txt"
Expand Down Expand Up @@ -142,6 +148,8 @@ def actionPerformed(self, event):
def openImage():
print rel_path
if rel_path.endswith(".klb"):
if(KLB==None):
print "Cannot open KLB due to missing module"
try:
klb = KLB.newInstance()
img = klb.readFull(os.path.join(base_path, rel_path))
Expand Down