Commit 41eb16b6 authored by Yi Sun's avatar Yi Sun
Browse files

make module number dynamic

parent 3039f751
......@@ -46,7 +46,7 @@ params = json.load(open(input_json_path, "r"))
def write_etss():
f.write(NEWLINE)
f.write("ExportToSpreadsheet:[module_num:6|svn_version:\\'Unknown\\'|variable_revision_number:12|show_window:True|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]"+NEWLINE)
f.write("ExportToSpreadsheet:[module_num:"+str(new_count)+"|svn_version:\\'Unknown\\'|variable_revision_number:12|show_window:True|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]"+NEWLINE)
f.write(FOURSPACES+"Select the column delimiter:"+params["delimiter"]+NEWLINE)
f.write(FOURSPACES+"Add image metadata columns to your object data file?:"+params["add_metadata_column_to_object"]+NEWLINE)
......@@ -97,7 +97,6 @@ def write_etss():
with open(input_pipeline) as fin:
lines = fin.readlines()
......
......@@ -75,6 +75,7 @@ input_json_path=sys.argv[1]
as_dict = json.load(open(input_json_path, "r"))
params=json.dumps(as_dict, indent=4, sort_keys=True)
with open("output","w") as f:
f.write(params)
......@@ -102,7 +103,7 @@ adv = params['con_advanced']['advanced']
def write_ipo():
f.write(NEWLINE)
f.write("IdentifyPrimaryObjects:[module_num:5|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:True|notes:\\x5B\\'Identify the nuclei from the DNA channel.\\', \\'PARAMS\\x3A\\', \\'- Typical diameter of objects (Min,Max)\\', \\'- Method to distinguish clumped objects\\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]"+NEWLINE)
f.write("IdentifyPrimaryObjects:[module_num:"+str(new_count)+"|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:True|notes:\\x5B\\'Identify the nuclei from the DNA channel.\\', \\'PARAMS\\x3A\\', \\'- Typical diameter of objects (Min,Max)\\', \\'- Method to distinguish clumped objects\\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]"+NEWLINE)
if adv == "Yes":
f.write(FOURSPACES+"Select the input image:"+ipo['input_from_nat']+NEWLINE)
......@@ -220,7 +221,7 @@ f.close()
</configfile>
</configfiles>
<command><![CDATA[
python $script_file $inputs $input_pipeline
python $script_file $inputs $input_pipeline
]]></command>
<inputs>
<param name="input_pipeline" type="data" label="Select pipeline file from previous moudle"/>
......
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