Added 2 menu plugins that allow the user to interactively use lipase
The 2 available plugins are: - Define Raw Images Root: this plugin allows the user to tell lipase where the raw images are stored - Estimate White: this plugin allows the user to trigger the computation of a white image estimate for the given sequence and the given channel (the sequence id an the channel ids are currently hardcoded but it is of course planned to make it user selectable) These changes involved quite a lot of work: - added the support of a lipase user settings file to store user dependent things such as the location of the lipase raw images (to allow the user to use lipase plugins without having to specify the raw images locations again an again) - investigations on how to make different lipase plugins use a common lipase library: the library is packagesd into a jar file placed in Fiji/jars/lib, while the plugins (menu items) are placed into Fiji/plugins directory - investigations on fiji script parameters (for plugins input output)
This commit is contained in:
parent
228ae4ab54
commit
e6217b38a3
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@ -0,0 +1,226 @@
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#!/bin/bash
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FIJI_ROOT_PATH='/Applications/Fiji.app'
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function ensure_maven_in_installed()
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{
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sudo port install maven32
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sudo port select --set maven maven32
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}
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function accept_maven_scijava_org_certificate()
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{
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# fixes (using the nice description in https://commandlinefanatic.com/cgi-bin/showarticle.cgi?article=art032) the following error when executing "mvn -Dimagej.app.directory=/Applications/Fiji.app"
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# [INFO] ------------------------------------------------------------------------
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# [ERROR] Failed to execute goal on project example-script-collection: Could not resolve dependencies for project org.scijava:example-script-collection:jar:0.1.0-SNAPSHOT: Failed to collect dependencies at net.imagej:imagej:jar:2.0.0-rc-71: Failed to read artifact descriptor for net.imagej:imagej:jar:2.0.0-rc-71: Could not transfer artifact net.imagej:imagej:pom:2.0.0-rc-71 from/to scijava.public (https://maven.scijava.org/content/groups/public): sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target -> [Help 1]
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# [ERROR]
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# [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
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local java_home=$(/usr/libexec/java_home)
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#[1]graffy@pr079234:~/toto/example-script-collection[15:43:02]>/usr/libexec/java_home
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#/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home
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local jre_home="$java_home/jre"
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keytool -list -keystore $jre_home/lib/security/cacerts
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# just press enter on the password prompt
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# [1]graffy@pr079234:~/toto/example-script-collection[15:44:43]>keytool -list -keystore /Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home/jre/lib/security/cacerts
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# Enter keystore password:
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# ***************** WARNING WARNING WARNING *****************
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# * The integrity of the information stored in your keystore *
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# * has NOT been verified! In order to verify its integrity, *
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# * you must provide your keystore password. *
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# ***************** WARNING WARNING WARNING *****************
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# Keystore type: JKS
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# Keystore provider: SUN
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# Your keystore contains 93 entries
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# digicertassuredidrootca, Apr 16, 2008, trustedCertEntry,
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# Certificate fingerprint (SHA1): 05:63:B8:63:0D:62:D7:5A:BB:C8:AB:1E:4B:DF:B5:A8:99:B2:4D:43
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# ...
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# godaddyrootg2ca, Jul 19, 2014, trustedCertEntry,
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# Certificate fingerprint (SHA1): 47:BE:AB:C9:22:EA:E8:0E:78:78:34:62:A7:9F:45:C2:54:FD:E6:8B
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keytool -printcert -rfc -sslserver maven.scijava.org
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# [1]graffy@pr079234:~/toto/example-script-collection[16:06:05]>keytool -printcert -rfc -sslserver maven.scijava.org
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# -----BEGIN CERTIFICATE-----
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# MIIFWDCCBECgAwIBAgISA7zwf4Rs4UhVp5fLyHh58bjtMA0GCSqGSIb3DQEBCwUAMEoxCzAJBgNV
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# ...
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# Ob5k02cDAcqlcJqIzqhxANh7UDoLw7h36hBnyIHDMbMMkfrtgMv5WSa0DZ2mZf63P6iYGUmr5dtz
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# ciAu0w==
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# -----END CERTIFICATE-----
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# -----BEGIN CERTIFICATE-----
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# MIIFWDCCBECgAwIBAgISA7zwf4Rs4UhVp5fLyHh58bjtMA0GCSqGSIb3DQEBCwUAMEoxCzAJBgNV
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# ...
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# Ob5k02cDAcqlcJqIzqhxANh7UDoLw7h36hBnyIHDMbMMkfrtgMv5WSa0DZ2mZf63P6iYGUmr5dtz
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# ciAu0w==
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# -----END CERTIFICATE-----
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# -----BEGIN CERTIFICATE-----
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# MIIEkjCCA3qgAwIBAgIQCgFBQgAAAVOFc2oLheynCDANBgkqhkiG9w0BAQsFADA/MSQwIgYDVQQK
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# ...
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# TZ+sOPAveyxindmjkW8lGy+QsRlGPfZ+G6Z6h7mjem0Y+iWlkYcV4PIWL1iwBi8saCbGS5jN2p8M
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# +X+Q7UNKEkROb3N6KOqkqm57TH2H3eDJAkSnh6/DNFu0Qg==
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# -----END CERTIFICATE-----
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# split output into:
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# - /tmp/cert1.pem
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# - /tmp/cert2.pem
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# - /tmp/cert3.pem
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keytool -importcert -file /tmp/cert1.pem -keystore $jre_home/lib/security/cacerts
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# password : changeit
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# [1]graffy@pr079234:~/toto/example-script-collection[17:12:30]>sudo keytool -importcert -file /tmp/cert1.pem -keystore $jre_home/lib/security/cacerts
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# Password:
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# Sorry, try again.
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# Password:
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# Enter keystore password:
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# Owner: CN=maven.imagej.net
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# Issuer: CN=Let's Encrypt Authority X3, O=Let's Encrypt, C=US
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# Serial number: 3bcf07f846ce14855a797cbc87879f1b8ed
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# Valid from: Sat Aug 17 07:39:53 CEST 2019 until: Fri Nov 15 06:39:53 CET 2019
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# Certificate fingerprints:
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# MD5: 05:B4:5A:31:AE:1F:36:71:0E:24:FB:0F:72:AE:BD:BD
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# SHA1: E5:3E:B0:CC:8E:D0:C6:A3:EF:2F:42:93:45:60:82:C2:1B:A3:BD:F3
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# SHA256: 74:3C:C7:2C:E6:C5:FE:9F:79:F5:F7:9D:7E:2A:4F:C9:BA:51:A0:88:95:1C:FC:15:8D:DC:EC:B0:99:BD:0E:61
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# Signature algorithm name: SHA256withRSA
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# Version: 3
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# Extensions:
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# #1: ObjectId: 1.3.6.1.4.1.11129.2.4.2 Criticality=false
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# 0000: 04 81 F2 00 F0 00 76 00 74 7E DA 83 31 AD 33 10 ......v.t...1.3.
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# 0010: 91 21 9C CE 25 4F 42 70 C2 BF FD 5E 42 20 08 C6 .!..%OBp...^B ..
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# 0020: 37 35 79 E6 10 7B CC 56 00 00 01 6C 9E 4D C8 C6 75y....V...l.M..
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# 0030: 00 00 04 03 00 47 30 45 02 20 1C DB D8 F3 9D 77 .....G0E. .....w
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# 0040: 48 BB B3 D7 0E 50 C4 0F C0 DF 65 94 A7 C4 23 E2 H....P....e...#.
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# 0050: 19 C3 88 4D 8D 6D D9 82 D3 BA 02 21 00 AC CC 93 ...M.m.....!....
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# 0060: BE 28 59 5C 2E BC A0 8E 36 4D 23 FB 1D 4B 0F FE .(Y\....6M#..K..
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# 0070: F4 38 9F C6 D1 13 53 91 62 25 0F C9 71 00 76 00 .8....S.b%..q.v.
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# 0080: 29 3C 51 96 54 C8 39 65 BA AA 50 FC 58 07 D4 B7 )<Q.T.9e..P.X...
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# 0090: 6F BF 58 7A 29 72 DC A4 C3 0C F4 E5 45 47 F4 78 o.Xz)r......EG.x
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# 00A0: 00 00 01 6C 9E 4D CA AD 00 00 04 03 00 47 30 45 ...l.M.......G0E
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# 00B0: 02 20 5B D4 50 BC 32 89 32 C4 33 EB 5B 30 3F 25 . [.P.2.2.3.[0?%
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# 00C0: F0 7C A6 D4 8A F7 8B AB 55 3A 54 6D F9 2E C9 DE ........U:Tm....
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# 00D0: D3 4B 02 21 00 8C A8 8B D3 38 20 38 A1 BB 37 B3 .K.!.....8 8..7.
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# 00E0: EE 3A 38 17 82 16 D3 1C E0 30 95 C4 E7 F7 8A 26 .:8......0.....&
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# 00F0: 62 B7 BC AF DF b....
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# #2: ObjectId: 1.3.6.1.5.5.7.1.1 Criticality=false
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# AuthorityInfoAccess [
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# [
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# accessMethod: ocsp
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# accessLocation: URIName: http://ocsp.int-x3.letsencrypt.org
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# ,
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# accessMethod: caIssuers
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# accessLocation: URIName: http://cert.int-x3.letsencrypt.org/
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# ]
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# ]
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# #3: ObjectId: 2.5.29.35 Criticality=false
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# AuthorityKeyIdentifier [
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# KeyIdentifier [
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# 0000: A8 4A 6A 63 04 7D DD BA E6 D1 39 B7 A6 45 65 EF .Jjc......9..Ee.
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# 0010: F3 A8 EC A1 ....
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# ]
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# ]
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# #4: ObjectId: 2.5.29.19 Criticality=true
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# BasicConstraints:[
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# CA:false
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# PathLen: undefined
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# ]
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# #5: ObjectId: 2.5.29.32 Criticality=false
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# CertificatePolicies [
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# [CertificatePolicyId: [2.23.140.1.2.1]
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# [] ]
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# [CertificatePolicyId: [1.3.6.1.4.1.44947.1.1.1]
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# [PolicyQualifierInfo: [
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# qualifierID: 1.3.6.1.5.5.7.2.1
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# qualifier: 0000: 16 1A 68 74 74 70 3A 2F 2F 63 70 73 2E 6C 65 74 ..http://cps.let
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# 0010: 73 65 6E 63 72 79 70 74 2E 6F 72 67 sencrypt.org
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# ]] ]
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# ]
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# #6: ObjectId: 2.5.29.37 Criticality=false
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# ExtendedKeyUsages [
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# serverAuth
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# clientAuth
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# ]
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# #7: ObjectId: 2.5.29.15 Criticality=true
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# KeyUsage [
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# DigitalSignature
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# Key_Encipherment
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# ]
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# #8: ObjectId: 2.5.29.17 Criticality=false
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# SubjectAlternativeName [
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# DNSName: maven.imagej.net
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# ]
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# #9: ObjectId: 2.5.29.14 Criticality=false
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# SubjectKeyIdentifier [
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# KeyIdentifier [
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# 0000: 63 09 5F EA C5 C8 7D 24 DD 2B 11 71 BB FB F6 F9 c._....$.+.q....
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# 0010: 6F 7C BD 0A o...
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# ]
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# ]
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# Trust this certificate? [no]: yes
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# Certificate was added to keystore
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#> mykey, Sep 20, 2019, trustedCertEntry,
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#> Certificate fingerprint (SHA1): E5:3E:B0:CC:8E:D0:C6:A3:EF:2F:42:93:45:60:82:C2:1B:A3:BD:F3
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#export MAVEN_OPTS="-Xmx512m -Djavax.net.ssl.trustStore=trust.jks \
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# -Djavax.net.ssl.trustStorePassword= \
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# -Djavax.net.ssl.keyStore=/tmp/cert1.pem \
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# -Djavax.net.ssl.keyStoreType=pem
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}
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function create_test_jar()
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{
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git clone https://github.com/imagej/example-script-collection.git
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pushd example-script-collection
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rm -R src/test/java
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ensure_maven_in_installed
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accept_maven_scijava_org_certificate
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mvn -Dimagej.app.directory=/Applications/Fiji.app
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popd
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}
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function install_lipase_libs_in_fiji()
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{
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# https://imagej.net/Jython_Scripting
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mkdir -p "$FIJI_ROOT_PATH/jars/Lib"
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# cp -R ./src/* "$FIJI_ROOT_PATH/jars/Lib"
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pushd src
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find ./lipase -name "*.py" > /tmp/files.txt
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jar cvf $FIJI_ROOT_PATH/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar @/tmp/files.txt
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popd
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}
|
||||
|
||||
function install_lipase_in_fiji()
|
||||
{
|
||||
install_lipase_libs_in_fiji
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||||
|
||||
mkdir -p $FIJI_ROOT_PATH/plugins/Ipr
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||||
rsync -a ./src/ij-plugins/Ipr/ $FIJI_ROOT_PATH/plugins/Ipr/
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}
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||||
|
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install_lipase_in_fiji
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@ -0,0 +1,27 @@
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#@ File (label="Select the root directory of root images", style="directory") RAW_IMAGES_ROOT_PATH
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# https://imagej.net/Script_Parameters
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# @ output String INFO
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# @File(label = "Image File", persist=True) FILENAME
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||||
"""This script is supposed to be launched from fiji's jython interpreter
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||||
"""
|
||||
# # note: fiji's jython doesn't support encoding keyword
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||||
# https://imagej.net/Scripting_Headless
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|
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from lipase.settings import UserSettings
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|
||||
# print("RAW_IMAGES_ROOT_PATH=%s", RAW_IMAGES_ROOT_PATH)
|
||||
|
||||
# it is necassary to add lipase's root path to the path if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
|
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# sys.path.append(lipase_src_root_path) # pylint: disable=undefined-variable
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def run_script():
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settings = UserSettings()
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settings.raw_images_root_path = str(RAW_IMAGES_ROOT_PATH)
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settings.save()
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# global INFO
|
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# INFO = "the root directory containing raw images (%s) has been stored in your settings file %s" % (str(RAW_IMAGES_ROOT_PATH), settings.get_settings_file_path())
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||||
# note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
|
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run_script()
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@ -0,0 +1,43 @@
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#@output ImagePlus WHITE_ESTIMATE
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"""This script is supposed to be launched from fiji's jython interpreter
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"""
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||||
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||||
#from ij import IJ # pylint: disable=import-error
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#WHITE_ESTIMATE = IJ.openImage('/Users/graffy/ownCloud/ipr/lipase/lipase.git/white_estimate.tiff')
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||||
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||||
# # note: fiji's jython doesn't support encoding keyword
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||||
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||||
# https://imagej.net/Scripting_Headless
|
||||
# String lipase_src_root_path
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||||
|
||||
# String(label="Please enter your name",description="Name field") name
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||||
# OUTPUT String greeting
|
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import sys
|
||||
print('python version %s' % sys.version) # prints python version
|
||||
|
||||
from lipase.settings import UserSettings
|
||||
|
||||
# it is necassary to add lipase's root path to the path if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
|
||||
# sys.path.append(lipase_src_root_path) # pylint: disable=undefined-variable
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||||
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||||
# from lipase import Lipase, ImageLogger
|
||||
from lipase.preprocessing import test_preprocessing # noqa: E402 pylint: disable=import-error,wrong-import-position
|
||||
from lipase.imageengine import IImageEngine
|
||||
from lipase.imagej.ijimageengine import IJImageEngine
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||||
from lipase.preprocessing import WhiteEstimator
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from lipase.catalog import ImageCatalog
|
||||
|
||||
def run_script():
|
||||
user_settings = UserSettings()
|
||||
IImageEngine.set_instance(IJImageEngine())
|
||||
catalog = ImageCatalog(user_settings.raw_images_root_path)
|
||||
sequence = catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
|
||||
white_estimator = WhiteEstimator(open_size=75, close_size=75, average_size=75)
|
||||
white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
|
||||
print(type(white_estimate))
|
||||
global WHITE_ESTIMATE
|
||||
WHITE_ESTIMATE = white_estimate.ij_image
|
||||
|
||||
# note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
|
||||
run_script()
|
||||
|
|
@ -15,7 +15,6 @@ from catalog import Sequence, ImageCatalog
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|||
import preprocessing
|
||||
# greeting = "Hello, " + name + "!"
|
||||
|
||||
|
||||
# image prefix :
|
||||
# AF
|
||||
# blé : coupes de blé
|
||||
|
|
@ -42,6 +41,8 @@ import preprocessing
|
|||
# - cond[5678] : condition non réalistes
|
||||
|
||||
|
||||
|
||||
|
||||
class IImageProcessingDebugger(object):
|
||||
|
||||
def __init__(self):
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
"""Lipase user settings."""
|
||||
import json
|
||||
from os.path import expanduser
|
||||
|
||||
|
||||
class UserSettings(object):
|
||||
"""User settings."""
|
||||
|
||||
attributes = {'raw_images_root_path': {'type': str}}
|
||||
|
||||
def __init__(self):
|
||||
"""constructor."""
|
||||
self.settings = {} # json dictionary
|
||||
self.raw_images_root_path = 'bla'
|
||||
try:
|
||||
with open(self.get_settings_file_path(), 'r') as json_file:
|
||||
self.settings = json.load(json_file)
|
||||
except IOError as error:
|
||||
print('Failed to read %s : %s' % (self.get_settings_file_path(), error))
|
||||
|
||||
def __getattr__(self, attr):
|
||||
"""Override __getattr__ to check the validity of settings attributes names."""
|
||||
print('getting %s' % (attr,))
|
||||
if attr == 'settings':
|
||||
return self.__dict__['settings']
|
||||
else:
|
||||
assert attr in UserSettings.attributes
|
||||
return self.settings[attr]
|
||||
|
||||
def __setattr__(self, attr, value):
|
||||
"""Override __setattr__ to check the validity of settings attributes names."""
|
||||
print('setting %s to %s' % (attr, value))
|
||||
if attr == 'settings':
|
||||
self.__dict__['settings'] = value
|
||||
else:
|
||||
assert attr in UserSettings.attributes
|
||||
assert type(value) == UserSettings.attributes[attr]['type'], "invalid type for attribute %s : %s instead of %s" % (attr, str(type(value)), str(UserSettings.attributes[attr]['type']))
|
||||
self.settings[attr] = value
|
||||
|
||||
def get_settings_file_path(self):
|
||||
"""Return the location of lipase user settings file."""
|
||||
home = expanduser("~")
|
||||
return '%s/.fr.univ-rennes1.ipr.lipase.json' % home
|
||||
|
||||
def save(self):
|
||||
"""Save user settings."""
|
||||
with open(self.get_settings_file_path(), 'w') as json_file:
|
||||
json.dump(self.settings, json_file)
|
||||
|
||||
|
||||
def test():
|
||||
"""Unit test."""
|
||||
settings = UserSettings()
|
||||
print(settings.raw_images_root_path)
|
||||
settings.raw_images_root_path = '/Users/graffy/ownCloud/ipr/lipase/raw-images'
|
||||
# settings.toto = 'hello'
|
||||
settings.save()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
test()
|
||||
Loading…
Reference in New Issue