We propose an automated camera setup for photogrammetric roughness analysis in the laboratory environment. The developed fast and low-cost automation setup can be very useful for tedious and laborsome manual field logging practices. The photographs are processed in MATLAB to obtain disparity maps. Coding routines for stereo photogrammetry and digital measurements are written in MATLAB. Secondly, 6 effecting factors (projecting an image onto core face, depth of field, brightness, camera-to-object to baseline distance ratio, projected image size and occlusion) influencing noise in roughness depth maps computed by employing stereo photogrammetry are investigated. After deciding the best values that allow the lowest amount of noise, depth maps of 6 core faces are computed. Using the 3D point cloud generated, roughness profile measurements are made. Then, 8 profile measurements are made for each core face, both manually and digitally. The accuracy of the disparity maps has been verified by comparing 48 joint roughness coefficient (JRC) measurements made manually using a profile gauge. It was proved that surface roughness can be measured very fast in millimetric accuracy with an average Root Mean Square Error (RMSE) of 3.50 and Mean Absolute Error (MAE) of 3.02 by the help of the proposed set-up and calibration.