Editing Scanco User Instructions (section)

===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']] 
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]


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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name 
*'''/aim_read''': 
*'''/read_versatile''': 
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''': 
*'''/write_part''': 
*'''/copy''':  Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''':   Deletes an internal file (a file that is already in the ipl system)
*'''/rename''':  Changes the name of the file (input is the old name and output the new name)
*'''/list''': 
*'''/options''': 
*'''/release_history''': 
*'''/commands_write_log''': 


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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''': 
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss.  A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range 
*'''/absolute_threshold''': 
*'''/adaptive_threshold''': 
*'''/adaptive_iter_threshold''': 
*'''/matching_threshold''': 


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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).  
*'''/gobj_circumf_area''': 
*'''/gobj_join''': 
*'''/gobj_join_consec''': 
*'''/gobj_scale''': 
*'''/gobj_isotrop''': 
*'''/cortex_maskoff''': 
*'''/peel3d''': 

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''': 
*'''/db_clear_eval''': 
*'''/db_calib_unit_fill''': 
*'''/db_set_mean_accur''': 
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points)  on the region within the gobj.  
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points. 
*'''/tri_da_metric_db''': 
*'''/tri_direc_distr''': 
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''': 
*'''/conn_bgcl''': 
*'''/fractal_dimension''': 

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''': 
*'''/dt_ow_object_param''': 
*'''/dt_background_param''': 
*'''/dt_mat_param''': 
*'''/dt_cortex_obj_param''': 
*'''/dt_value_output''': 
*'''/dt_mat_output''': 

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''': 
*'''/moment2d_of_inertia''': 
*'''/moment3d_of_inertia''': 
*'''/zmeanmax''': 

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====Voxelsize-Scaling Functions====
*'''/isotrop''': 
*'''/scale_elsize''': 
*'''/ipscale_elsize''': 
*'''/noipscale_elsize''': 
*'''/scale_ow_elsize_noip''': 

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''': 
*'''/cl_image''': 
*'''/cl_extract''': 
*'''/cl_slicewise_extractow''': 
*'''/cl_nr_extract''': 

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''': 
*'''/border_change''': 
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them.  The data from both aims or just the common region can be kept.  To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''': 
*'''/divide_volumes''': 
*'''/fill_min_max_ow''': 
*'''/header_geo_set''': 
*'''/header_log_set''': 
*'''/header_calib_ov''': 
*'''/invert_ow''': 
*'''/mult_constant_ow''': 
*'''/multiply_volumes''': 
*'''/sqr_to_float''': 
*'''/sqrt_to_float''': 
*'''/offset_add''': 
*'''/offset_set''': 
*'''/clear_offset''': 
*'''/fill_offset_mirror''': 
*'''/fill_offset_duplicate''': 
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image <br />
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates <br />
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) <br />
**indexing starts at 0 instead of 1
*'''/sub_pick''': 
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region. 
*'''/sup_divide''': 
*'''/transparent_concat''': 

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====Erosion Dilation Open Close Functions====
*'''/erosion''': 
*'''/dilation''': 
*'''/open''': 
*'''/close''': 
*'''/erosion_dilat_variable''': 

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''': 
*'''/dicom_to_aim''': 
*'''/todicom_from_aim''': 
*'''/dicom_list_series''': 
*'''/isq_to_aim''': 
*'''/isq_gobjfit_to_aim''': 
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file.  The isq name should be 8 characters long.  
*'''/mesh''': 
*'''/msq_from_aim''': 
*'''/rsq_to_aim''': 
*'''/stl_tri''': 
*'''/convert_to_type''': 
*'''/convert_unsigned''': 
*'''/norm_max''': 

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====Functions for Root Canal Evaluations====
*'''/separ_roots''': 
*'''/calc_ctr_mass_list''': 
*'''/calc_ctr_mass_diff''': 
*'''/treated_surf''': 
*'''/match_cut''': 
*'''/match_cut_adapt''': 

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====Miscellaneous Functions====
*'''/align_z''': 
*'''/dcl''': 
*'''/flip_aim''': 
*'''/growback_to_orig''': 
*'''/turn3d''': 
*'''/turn2d''': 
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''': 

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''': 
*'''/cut2D_shape_ow''': 
*'''/join_uncompress''': 
*'''/mil_param''': 
*'''/milv1_param''': 
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq 
*'''/local_threshold''': 
*'''/edge_canny''': 
*'''/sobel_grad''': 
*'''/hysteresis_thresholg''': 

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input  1. Gobjs can be input (registration is more successful with gobjs).  Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals. 
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input).  Interpolation options are nearest neighbor, linear, and cubic interpolation.  The inverse of the transform provided can be done by setting Tmat_invert to true.  
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here


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