The python executable for PATMOS is

PATMOS_MIDOM_200324.zip

This alone cannot run ORB_SLAM2 but it can visualize the data and allow the user to hand track the environment.  To load the virtual Linux environment that has ORB_SLAM2 and PATMOS already set up use this file.

This is the Virtual Box Appliance file to load this Linux version on your computer. 

patmos.ova

The instructions on how to use these and install these files are in “Manual for PATMOS_MIDOM 200414.docx”

You will then have to modify the ProjectMain.xlsx file as discussed in the Manual.

To visualize the data using the PATMOS executable you need to put all these files from Dryad into the same folder that you will specify in ProjectMain.xlsx:

 

Riparian environment:

Project name in ProjectMain.xlsx: tom_245_jill_189_v1

h5 files

example_GoProJill_187_H.h5

example_GoProJill_189_H.h5

example_GoProTom_243_H.h5

example_GoProTom_245_H.h5

data_tom245_jill189.H5

map files:

tomGP243_ltp0001rgb_topcut.stl

tomGP243_ltp0001rgb_topcut.txt

 

Marble dropping environment:

Project name in ProjectMain.xlsx: jill_320_tom_376

h5 files:

data_jill_320_tom_376_2.h5

metadata_jill_320_HCO.h5

metadata_tom_376_HCO.h5

map files

ML_ORB_jill_320_tom_376.txt

ML_ORB_jill_320_tom_376.stl

 

And for running the ORB_SLAM2 in Virtual Box you will need to put these files from Dryad in the same video folder:

Riparian environment:

GoProJill/GOPR0187.MP4

GoProJill/GOPR0189.MP4

goprotom/GOPR0243.MP4

goprotom/GOPR0245.MP4

 

Marble dropping environment:

GoProJill/GOPR0320.MP4

goprotom/GOPR0376.MP4

 

There should also be some preloaded map files for some of these projects in the Ubuntu file including this one for the marble drop experiment Map_ORB_jill_320_tom_376.bin

 

ProjectMain

Figure 2

Path data for blender visualization

Amberwing path data:

For visualizing paths over meshes in blender.

filenameq_CSV_MeshLab_rainbowandBlack.txt

This consists of six paths that have been broken up into mirrored and regular counterparts.

The blender file the paths have been rendered in:

Amberwing5Vslam.blend

The OpenMVS mesh file of the environment.

scene_dense_mesh_textureML_AW.obj

The STL was derived from KeyFrameTrajectory_tom_318_jill_261_190115_cleanup3.txt

The waterplane was derived from KeyFrameTrajectory_tom_318_jill_261_190115_water_200522.txt

The ORBSTL is KeyFrameTrajectory_tom_318_jill_261_190115_cleanup3.stl

 

Damselfish:

The blender file is:

DamselVsOCtRefined2.blend

The OpenMVS mesh is:

scene_dense_mesh_refine_texture_DF.obj

 

Figure 3:

The data for this figure is in FiducialDistribution.xlsx

Graphed in Graphing_Fiducial_Distribution4BBpaper.py

 

Distance between cameras:

 

ORB_SLAM2 measured data in it:

Distance between Cameras.xlsx

 

The Physical measurements for the measurement rig:

camera distances measured.xlsx

 

The graphs were made in Graphing_Distance2STL_4Paper.py

 

Figure 4:

Marble dropping related figure: 

Blender file:

marbelsRefined_withGoProSTL4.blend

 

Marble data statistics:

Statistics from the graph coming from MarblesAngle_vs_g_and_errorDistance201021y.py:

General marble statistics:

marble statisticsBBresub.xlsx

 

Figure 5:

The distance of paths to STL plots:

The graphs are made in Graphing_Distance2STL_4Paper.py

Amberwing:

Z-direction distance

Amberwing13_INFO.xls

Amberwing43_INFO.xls

 

Damselfish:

Full Distance to STL.

This is the OpenMVS STL distance without error.

DamselPathsMVSn2_INFO.xls

This is the PATMOS STL distance with error.

DamselPathsn2_INFO.xls

 

Figure 6:

Data are deposited in Sam_20377RC_Sky_20232RCFR_fh5_MapCovisibilityCharacteriztion_INFO.xls

 

Sup Figure 1:

The map error graph is meant to give a complete idea of the map's error and reliability.

This graph consists of:

1. Map points in percentage levels
2. Camera position colored with the same levels and joined together with a line
3. The fiducial object with map points
4. Color underlay of map errors
5. The paths are put in there with the error with the same scaling as the background error estimate.

 

Amberwing:

tom_319_jill_262_F_MapCharacteriztion_INFO.xls

Marbles:

jill_320_tom_376_2_MapCharacteriztion_INFO.xls

Damselfish:

Sam_20377RC_Sky_20232RCFR_fh5_MapCharacteriztion_INFO.xls

 

Sup Figure 2:

Difference between openMVS maps and PATMOS maps

 

Damselfish:

The map is:

scene_dense_mesh_refine_texture_DF.obj

 

The map is compared with scene_dense_mesh_refine_Damselnew.stl

The disparity information is in a numpy array saved in:

Damseldisparitymap.npy

and in dictionary form, listing a ; separated value with x;y;(distance between STL):

DamseldisparitymapDict.npy

Blender file:

DamselMapComparison3_viridis.blend

 

Marbles

The map is compared with the OpenMVS map:

scene_dense_mesh_refine_Marbles5Rescale.stl

The disparity information is in a numpy array saved in:

marbledisparitymap.npy

and in dictionary form, listing a ; separated value with x;y;(distance between STL):

MarbledisparitymapDict.npy

Blender file:

marbelsMapComparisonnewcolor_newColor.blend

 

Amberwing:

Amberdisparitymap.npy

and in dictionary form, listing a ; separated value with x;y;(distance between STL):

AmberdisparitymapDict.npy

 

The disparity stats calculation is done in Displarity_path_calculation.py

Blender file:

Amberwing7Vslam_viridis.blend

 

Other Statistical results not in figures:

 

Mean time and path length of falling marbles

Found in the general info sheet in:

marPathLength_INFO.xls

 

Maps associated with these projects

Amberwing:

The map for the amber wing data was not very good.   It did not refine in OpenMVS, It did not include the water surface where the amberwings were found flying, and it did not give good results of the branches in the water.

 

The map used for blender was:

scene_dense_mesh_textureML_AW.obj

other versions:

scene_dense_mesh_Amberwing3.stl

and was put in the Red folder Maps and rescaled to:

scene_dense_mesh_Amberwing3Rescale.stl

The stl was derived from KeyFrameTrajectory_tom_318_jill_261_190115_cleanup3.txt

The water plane was derived from KeyFrameTrajectory_tom_318_jill_261_190115_water_200522.txt

 

Damselfish:

OpenMVS file is:

scene_dense_mesh_refine_Damsel.stl

and is rescaled as:

scene_dense_mesh_refine_Damselnew.stl

The PATMOS STL was derived from KFT_ORB_Sam_20377RC_Sky_20232RC_cut.txt

That has various parts of the point cloud cut.

The PATMOS SLT with error are:

KFT_ORB_Sam_20377RC_Sky_20232RC_cut.stl

KFT_ORB_Sam_20377RC_Sky_20232RC_cut_err.npy

 

Marbles:

The OpenMVS mesh is scene_dense_mesh_refine_texture_Mar.obj

scene_dense_mesh_refine_Marbles5.stl

rescaled

scene_dense_mesh_refine_Marbles5Rescale.stl

 

For the ORB_STL:

Use as an input ML_ORB_jill_320_tom_376_2.txt:

The PATMOS SLT with error are:

 

ML_ORB_jill_320_tom_376_2.stl

ML_ORB_jill_320_tom_376_2_err.npy

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