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saalfeldlab / paintera

GNU General Public License v2.0
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Unable to open paintera project (NumberFormatException) #440

Closed bogovicj closed 2 years ago

bogovicj commented 2 years ago

On opening a paintera project, I get

this error:

java.lang.NumberFormatException: For input string: "seed"
    at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.base/java.lang.Long.parseLong(Long.java:692)
    at java.base/java.lang.Long.parseLong(Long.java:817)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer$Companion.toColorMap(ConnectomicsLabelState.kt:885)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer$Companion.access$toColorMap(ConnectomicsLabelState.kt:884)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer$deserialize$$inlined$with$lambda$6$1.invoke(ConnectomicsLabelState.kt:871)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer$deserialize$$inlined$with$lambda$6$1.invoke(ConnectomicsLabelState.kt:824)
    at org.janelia.saalfeldlab.paintera.serialization.GsonExtensions$Companion.letJsonObject(GsonExtensions.kt:77)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer$deserialize$$inlined$with$lambda$6.invoke(ConnectomicsLabelState.kt:871)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer$deserialize$$inlined$with$lambda$6.invoke(ConnectomicsLabelState.kt:824)
    at org.janelia.saalfeldlab.paintera.serialization.GsonExtensions$Companion.letJsonObject(GsonExtensions.kt:77)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer.deserialize(ConnectomicsLabelState.kt:869)
    at org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState$Deserializer.deserialize(ConnectomicsLabelState.kt:824)
    at com.google.gson.internal.bind.TreeTypeAdapter.read(TreeTypeAdapter.java:69)
    at com.google.gson.Gson.fromJson(Gson.java:932)
    at com.google.gson.Gson.fromJson(Gson.java:1003)
    at com.google.gson.Gson.fromJson(Gson.java:975)
    at org.janelia.saalfeldlab.paintera.serialization.SourceInfoSerializer.makeStates(SourceInfoSerializer.java:180)
    at org.janelia.saalfeldlab.paintera.serialization.SourceInfoSerializer.populate(SourceInfoSerializer.java:114)
    at org.janelia.saalfeldlab.paintera.PainteraMainWindow.deserialize(PainteraMainWindow.kt:348)
    at org.janelia.saalfeldlab.paintera.PainteraMainWindow.deserialize(PainteraMainWindow.kt:202)
    at org.janelia.saalfeldlab.paintera.Paintera.start(Paintera.kt:60)
    at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:846)
    at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:474)
    at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:447)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:446)
    at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
    at javafx.graphics/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
    at javafx.graphics/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:277)
    at java.base/java.lang.Thread.run(Thread.java:829)

the attributes.json in my paintera project folder:

{
  "n5": "2.5.0",
  "paintera": {
    "globalTransform": [
      11.834009081934655,
      0.0,
      0.0,
      -1212.9745035012422,
      0.0,
      11.834009081934624,
      0.0,
      -1643.918763852703,
      0.0,
      0.0,
      11.834009081934655,
      -1937.1733080212516
    ],
    "windowProperties": {
      "width": 1360,
      "height": 743,
      "isFullScreen": false
    },
    "crosshairConfig": {
      "onFocusColor": "#FFFFFFFF",
      "offFocusColor": "#808080FF",
      "isVisible": false
    },
    "orthoSliceConfig": {
      "enabled": true,
      "showTopLeft": true,
      "showTopRight": true,
      "showBottomLeft": true,
      "opacity": 1.0,
      "shading": 0.1,
      "bottomLeftViewIndex": 2
    },
    "navigationConfig": {
      "allowRotations": true,
      "buttonRotationSpeeds": {
        "slow": 0.5,
        "regular": 5.0,
        "fast": 45.0
      }
    },
    "viewer3DConfig": {
      "affine": [
        0.001674279285131773,
        5.87412761345254E-5,
        -1.6588024659292057E-4,
        -0.4905071064552835,
        0.0,
        0.0015869385371922189,
        5.619644094844643E-4,
        -0.27648403354438134,
        1.759738438849385E-4,
        -5.588859096500019E-4,
        0.0015782451218413606,
        -0.11652273855109026
      ],
      "areMeshesEnabled": true,
      "background": "#000000FF",
      "showBlockBoundaries": false,
      "rendererBlockSize": 16,
      "numElementsPerFrame": 10000,
      "frameDelayMsec": 20,
      "sceneUpdateDelayMsec": 250
    },
    "screenScalesConfig": {
      "scales": [
        1.0,
        0.5,
        0.25,
        0.125,
        0.0625
      ]
    },
    "scaleBarOverlayConfig": {
      "overlayFont": {
        "name": "System Regular",
        "size": 18.0
      },
      "foregroundColor": "#FFFFFFFF",
      "backgroundColor": "#00000088",
      "isShowing": false,
      "targetScaleBarLength": 200.0
    },
    "bookmarkConfig": {
      "transitionTime": {
        "millis": 300.0
      }
    },
    "arbitraryMeshConfig": {
      "isVisible": false,
      "meshes": []
    },
    "gridConstraints": {
      "previousFirstRowHeight": 50.0,
      "previousFirstColumnWidth": 50.0,
      "isFullScreen": true,
      "firstRowHeight": 100.0,
      "firstColumnWidth": 100.0
    },
    "menuBarConfig": {
      "isVisible": true,
      "mode": "OVERLAY"
    },
    "sideBarConfig": {
      "isVisible": true,
      "width": 287.0
    },
    "statusBarConfig": {
      "isVisible": true,
      "mode": "OVERLAY"
    },
    "loggingConfig": {
      "isLoggingEnabled": false,
      "isLoggingToConsoleEnabled": false,
      "isLoggingToFileEnabled": false
    },
    "multiBoxOverlayConfig": {
      "visibility": "OFF"
    },
    "sourceInfo": {
      "sources": [
        {
          "type": "org.janelia.saalfeldlab.paintera.state.raw.ConnectomicsRawState",
          "state": {
            "backend": {
              "type": "org.janelia.saalfeldlab.paintera.state.raw.n5.N5BackendRaw",
              "data": {
                "container": {
                  "type": "org.janelia.saalfeldlab.n5.N5FSWriter",
                  "data": {
                    "basePath": "/home/john/projects/flyem_malebrain/seg/segdata.n5"
                  }
                },
                "dataset": "/raw"
              }
            },
            "name": "raw",
            "composite": {
              "type": "org.janelia.saalfeldlab.paintera.composition.CompositeCopy",
              "data": {}
            },
            "converter": {
              "min": 0.0,
              "max": 2000.0,
              "alpha": 1.0,
              "color": "#FFFFFF"
            },
            "interpolation": "NEARESTNEIGHBOR",
            "isVisible": true,
            "resolution": [
              0.44,
              0.44,
              0.44
            ]
          }
        },
        {
          "type": "org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState",
          "state": {
            "backend": {
              "type": "org.janelia.saalfeldlab.paintera.state.label.n5.N5BackendSingleScaleDataset",
              "data": {
                "container": {
                  "type": "org.janelia.saalfeldlab.n5.N5FSWriter",
                  "data": {
                    "basePath": "/home/john/projects/flyem_malebrain/seg/segdata.n5"
                  }
                },
                "dataset": "/left",
                "fragmentSegmentAssignment": {
                  "actions": []
                }
              }
            },
            "name": "left",
            "meshSettings": {
              "globalSettings": {
                "numScaleLevels": 1
              }
            },
            "composite": {
              "type": "org.janelia.saalfeldlab.paintera.composition.ARGBCompositeAlphaYCbCr",
              "data": {}
            },
            "converter": {
              "seed": 22,
              "userSpecifiedColors": {
                "0": "#1A1A1AFF",
                "1": "#FF00FFFF",
                "2": "#00FF00FF",
                "3": "#FF6666FF"
              }
            },
            "interpolation": "NEARESTNEIGHBOR",
            "isVisible": true,
            "resolution": [
              0.44,
              0.44,
              0.44
            ],
            "labelBlockLookup": {
              "type": "NO_BLOCKS"
            }
          }
        }
      ],
      "currentSourceIndex": 1,
      "numSources": 2
    },
    "version": "0.29.1"
  }
}
bogovicj commented 2 years ago

This happens after I set "Custom Colors" in the color conversion menu for a label source

cmhulbert commented 2 years ago

@bogovicj I believe this was addressed with the most recent release Paintera 0.30.0