Field - haimeh/finFindR GitHub Wiki

Field

Preprocessing Raw Field Images

By selecting Field as the Input Type you will be presented with the folowing panel: alt text
The Crop button begins the process and iterates through all images in the location typed into in the Query Directory box. A progress bar will appear in the lower right. The app also iterates through sub directories within the Query Directory if any are present.
As each image is processed, the crops are saved in a new directory which duplicates the the structure of the Query Directory.
The Query Directory is "12_09_14" in the following diagram. finFindR creates a new directory "12_09_14_finFindR-Crops" where the crops are saved. Note how the names and structure of the directory are preserved.
The image names are also preserved but with the addition of a "_1.jpg" or "_2.jpg". These additions indicate the number of fins found in the image. For most images in the below example, there was only 1 fin with a few exceptions where there were two or none. 

├───12_09_14
│   ├───S1_07-13-15
│   │   └───101EOS1D
│   │           S1 S1 006.JPG
│   │           S1 S1 007.JPG
│   │           S1 S1 008.JPG
│   │           S1 S1 009.JPG
│   │           S1 S1 010.JPG
│   │
│   ├───S2_07-14-15
│   │   ├───106CANON
│   │   │       S2 S6 092.JPG
│   │   │       S2 S6 093.JPG
│   │   │       S2 S6 094.JPG
│   │   │       S2 S6 095.JPG
│   │   │
│   │   └───107CANON
│   │           S2 S7 105.JPG
│   │           S2 S7 106.JPG
│   │           S2 S7 107.JPG
│   │           S2 S7 108.JPG
│   │
│   └───S3_07-15-15
│       └───101EOS1D
│               S3 S1 001.JPG
│               S3 S1 002.JPG
│               S3 S1 003.JPG
│               S3 S1 004.JPG
│               S3 S1 005.JPG
│
└───12_09_14_finFindR-Crops
    ├───S1_07-13-15
    │   └───101EOS1D
    │           S1 S1 006_1.jpg
    │           S1 S1 007_1.jpg
    │           S1 S1 008_1.jpg
    │           S1 S1 009_1.jpg
    │           S1 S1 010_1.jpg
    │           S1 S1 010_2.jpg
    │
    ├───S2_07-14-15
    │   ├───106CANON
    │   │       S2 S6 095_1.jpg
    │   │
    │   └───107CANON
    │           S2 S7 105_1.jpg
    │           S2 S7 106_1.jpg
    │           S2 S7 107_1.jpg
    │           S2 S7 108_1.jpg
    │
    └───S3_07-15-15
        └───101EOS1D
                S3 S1 002_1.jpg
                S3 S1 002_2.jpg
                S3 S1 003_1.jpg
                S3 S1 003_2.jpg
                S3 S1 004_1.jpg
                S3 S1 005_1.jpg

Field mode also offers the ability to change the sensitivity via the Threshold: slider bar. If the app is cropping too many false positives, you can increase the threshold and if the app is missing fins, you can decrease the threshold.
There is also the option to crop tightly around the fin or to include any visible body via the CropType buttons.

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