This package is a compilation of functions to analyze orthomosaic images from research fields. To prepare the image it first allows to crop the image, remove soil and weeds and rotate the image. The package also builds a plot shapefile in order to extract information for each plot to evaluate different wavelengths, vegetation indices, stand count, canopy percentage, and plant height.
#### 1. First steps > **Taking the first step:** wzxhzdk:10 [Menu](#menu)
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> **Attention:** The plots are identified in ascending order from *left to right* and *bottom to top* (this is another difference from the **`FIELDimageR::fieldShape`** ) being evenly spaced and distributed inside the selected area independent of alleys.
> One matrix can be used to identify the plots position according to the image above. The function **`fieldMap`** can be used to specify the plot *ID* automatic or any other matrix (manually built) also can be used. For instance, the new column **PlotName** will be the new identification. You can download an external table example here: [DataTable.csv](https://drive.google.com/open?id=18YE4dlSY1Czk2nKeHgwd9xBX8Yu6RCl7). wzxhzdk:15
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> *Sugestion:* This function could also be used to build an index to remove soil or weeds. First it is necessary to identify the threshold to differentiate soil from the plant material. At the example below (B), all values above 0.7 were considered as soil and further removed using **`fieldMask`** (C & D). wzxhzdk:19
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> To refine stand count, we can further eliminate weeds (small plants) or outlying branches from the output using the parameter *min Size*. The following example uses an image available to download here:[EX_StandCount.tif](https://drive.google.com/open?id=1PzWcIsYQMxgEozR5HHUhT0RKcstMOfSk) wzxhzdk:22
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> **`fieldCount`** also can be used to count other objects (e.g. seed, pollen, etc). The example below *FIELDimageR* pipeline was used to count seeds in a corn ear.
> **`fieldMask`** with index BIM (Brightness Index Modified) was used to identify pollen and **`fieldCount`** was used to count total and germinated pollens per sample. [Download EX_Pollen.jpeg](https://drive.google.com/open?id=1Tyr4cEvEBoaWqaHw8UWPW-X1unzEMAfk) wzxhzdk:25
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> **`fieldArea`** also can be associated with the function **`fieldMask`** to evaluate the proportion of seed colors in Glass Gems Maize. An important step is to choose the right contrasting background to differentiate samples. The same approach can be used to evaluate the percentage of disease/pests’ damage, land degradation, deforestation, etc.
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### Creating interpolated mosaics based on sampled points > Attention: In case the user has only one flight (e.g., one DSM) the function **`fieldInterpolate`** can be used to creat the soil-reference based on sampled points at the DSM1. wzxhzdk:29
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> The function **`fieldCrop`** can be used to remove objects from the field image. For instance, the parameter *remove=TRUE* and *nPoint* should be used to select the object boundaries to be removed. [Download EX_RemObj.tif](https://drive.google.com/open?id=1wfxSQANRrPOvJWwNZ6UU0UjXwzKfkKH0)). wzxhzdk:31
> The function **`fieldDraw`** can be used to draw lines or polygons in the field image. This function allows to extract information of specific positions in the field (x, y, value). Also, this function can be used to evaluate distances between objects (for example: distance between plants in a line) or either objects length (for example: seed length, threes diameter, etc.). Let's use the image above to evaluate the distance between potato plots and later to extract NGRDI values from a line with soil and vegetation to observe the profile in a distance plot. wzxhzdk:32
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