initial setup#

There are a number of files that you will need to process your images using MicMac, which are detailed below.

MicMac-LocalChantierDescripteur.xml#

Note

The following explains the use of spymicmac.micmac.create_localchantier_xml() or create_localchantier_xml to generate this file.

Alternatively, you can download and edit the example file linked below.

To create the MicMac-LocalChantierDescripteur.xml file, you need the following information:

name - This is the name that is used in the AutoCal.xml file that describes the camera parameters, so it should be as short as possible and without spaces.
short_name - a (longer) description of the camera
film_size - the film size [width, height] in mm. This should be the size of the image frame after resampling using the fiducial markers - for example, xmax - xmin, ymax - ymin for the maximum/minimum x,y position of the fiducial markers.
pattern - the file matching pattern to use for the images. Use '.*' to match all images in the directory.
focal - the nominal focal length for the camera, in mm.
add_sfs - whether to use SFS matching to help find tie points in low-contrast images.
cam_csv - an optional name of a CSV file that defines multiple cameras, if attempting to process images from multiple cameras at once (see more information below).

MeasuresCamera.xml#

Warning

This file must be placed in a directory called Ori-InterneScan in order for MicMac to be able to use it.

Ideally, you will have a camera calibration report, that will tell you the location of the different fiducial markers in the image geometry. Note that using ReSampFid requires a file, Ori-InterneScan/MeasuresCamera.xml, that tells MicMac what the location of each fiducial mark is.

Note

The image coordinates are defined with the origin in the upper left corner, rather than the center of the image used by most calibration files. You can translate from one system to the other with the following:

xp = x - min(x)
yp = (-y) - min(-y)

If you do not have a calibration report for your particular camera, you can have a look at some example fiducial marker patterns for approximate locations of fiducial markers.

Rather than editing the MeasuresCamera.xml file with the fiducial marker locations, you can also put the fiducial marker locations into a CSV file like this:

gcp,im_col,im_row
P1,-105.99,-105.994
P2,106.002,106.004
P3,-105.996,106.003
P4,106.012,-105.994
P5,-109.998,0.005
P6,109.997,0.009
P7,0.004,109.996
P8,0.009,-109.995

Then, use spymicmac.micmac.create_measurescamera_xml() to create Ori-InterneScan/MeasuresCamera.xml:

from spymicmac import micmac
micmac.create_measurescamera_xml(fn_csv, translate=True)

This will generate the following XML file:

<?xml version='1.0' encoding='UTF-8'?>
<SetOfMesureAppuisFlottants>
  <MesureAppuiFlottant1Im>
    <NameIm>Glob</NameIm>
    <OneMesureAF1I>
      <NamePt>P1</NamePt>
      <PtIm>4.00800000000001 215.99</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P2</NamePt>
      <PtIm>216.0 3.9919999999999902</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P3</NamePt>
      <PtIm>4.0020000000000095 3.992999999999995</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P4</NamePt>
      <PtIm>216.01 215.99</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P5</NamePt>
      <PtIm>0.0 109.991</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P6</NamePt>
      <PtIm>219.995 109.987</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P7</NamePt>
      <PtIm>110.00200000000001 0.0</PtIm>
    </OneMesureAF1I>
    <OneMesureAF1I>
      <NamePt>P8</NamePt>
      <PtIm>110.007 219.99099999999999</PtIm>
    </OneMesureAF1I>
  </MesureAppuiFlottant1Im>
</SetOfMesureAppuisFlottants>

id_fiducial.txt#

This is just a plain text file, with the “names” of the different fiducial marks:

P1
P2
P3

… and so on. You can easily generate this from the command line:

for nn in {1..8}; do echo P$nn >> id_fiducial.txt; done

Alternatively, in python:

with open('id_fiducial.txt', 'w') as f:
    for nn in range(1, 9):
        print(f"P{nn}", file=f)

Making sure to adjust the number of fiducials based on your camera.

Note

The names in the file must match the names written in MeasuresCamera.xml.

file structure#

Before starting, your file structure should look something like this:

project
├── id_fiducial.txt
├── Img1.tif
├── Img2.tif
...
├── MicMac-LocalChantierDescripteur.xml
├── Ori-InterneScan
│   └── MeasuresCamera.xml

Once you have this set up, you can work on the preprocessing steps.

example micmac files#

Below, you can download some example files to get started with your MicMac project. Note you will most likely need to modify them as explained above.

multiple cameras#

spymicmac also provides some tools for setting up multiple cameras for processing at the same time. spymicmac.micmac.generate_multicam_csv() will create a CSV based on multiple input parameters. You can either generate the CSV directly:

from spymicmac import micmac
micmac.generate_multicam_csv(
    patterns = ['AR1VDYL.*', 'ARH61.*', 'AR58.*', 'AR1QM.*'],
    fn_out = 'camera_defs.csv',
    name = ['AR1VDYL', 'ARH61', 'AR58', 'AR1QM'],
    short_name = ['Wild RC8', 'Zeiss RMK A 15/23', 'Wild RC10', 'Hurd + Metrogon'],
    film_width = [220.000, 225.969, 219.995, 217.750],
    film_height = [220.009, 225.992, 219.992, 217.750],
    focal = [152.22, 152.335, 302.281, 151.1]
)

Note

Alternatively, you can run this with no arguments to generate a blank CSV template that you can edit:

from spymicmac import micmac
micmac.generate_multicam_csv()

Once you have a CSV with multiple camera definitions, run spymicmac.micmac.create_localchantier_xml(), passing the filename of your CSV with the cam_csv argument:

from spymicmac import micmac
micmac.create_localchantier_xml(cam_csv='camera_defs.csv', add_sfs=True)

This will then create the MicMac-LocalChantierDescripteur.xml file with multiple cameras defined:

<?xml version='1.0' encoding='UTF-8'?>
<Global>
  <ChantierDescripteur>
    <LocCamDataBase>
      <CameraEntry>
        <Name>AR1VDYL</Name>
        <SzCaptMm>220.000 220.009</SzCaptMm>
        <ShortName>Wild RC8</ShortName>
      </CameraEntry>
      <CameraEntry>
        <Name>ARH61</Name>
        <SzCaptMm>225.969 225.992</SzCaptMm>
        <ShortName>Zeiss RMK A 15/23</ShortName>
      </CameraEntry>
      <CameraEntry>
        <Name>AR58</Name>
        <SzCaptMm>219.995 219.992</SzCaptMm>
        <ShortName>Wild RC10</ShortName>
      </CameraEntry>
      <CameraEntry>
        <Name>AR1QM</Name>
        <SzCaptMm>217.7500 217.750</SzCaptMm>
        <ShortName>Hurd + Metrogon</ShortName>
      </CameraEntry>
    </LocCamDataBase>
    <KeyedNamesAssociations>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_AR1VDYL.*</PatternTransform>
          <CalcName>AR1VDYL</CalcName>
        </Direct>
      </Calcs>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_ARH61.*</PatternTransform>
          <CalcName>ARH61</CalcName>
        </Direct>
      </Calcs>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_AR58.*</PatternTransform>
          <CalcName>AR58</CalcName>
        </Direct>
      </Calcs>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_AR1QM.*</PatternTransform>
          <CalcName>AR1QM</CalcName>
        </Direct>
      </Calcs>
      <Key>NKS-Assoc-STD-CAM</Key>
    </KeyedNamesAssociations>
    <KeyedNamesAssociations>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_AR1VDYL.*</PatternTransform>
          <CalcName>152.22</CalcName>
        </Direct>
      </Calcs>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_ARH61.*</PatternTransform>
          <CalcName>152.335</CalcName>
        </Direct>
      </Calcs>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_AR58.*</PatternTransform>
          <CalcName>302.281</CalcName>
        </Direct>
      </Calcs>
      <Calcs>
        <Arrite>1 1</Arrite>
        <Direct>
          <PatternTransform>OIS-Reech_AR1QM.*</PatternTransform>
          <CalcName>151.1</CalcName>
        </Direct>
      </Calcs>
      <Key>NKS-Assoc-STD-FOC</Key>
    </KeyedNamesAssociations>
  </ChantierDescripteur>
</Global>

Tools such as Tapas will then calibrate the intrinsic parameters for each camera separately.

Note

If you are processing images from multiple cameras simultaneously, you should still do the geometric processing for the images from each camera separately. Once the images have been resampled, you can proceed with steps like Tapioca and Tapas with all of the resampled images in the same directory.

initial setup

Contents

initial setup#

MicMac-LocalChantierDescripteur.xml#

MeasuresCamera.xml#

id_fiducial.txt#

file structure#

example micmac files#

multiple cameras#