U R/Bf@szddlZddlmZddlTddlTddlZddlZddl m Z ddZ ddZ d d Z d d Zd dZedkrvedS)N) euclidean)*)argvcCs@tdt|D],}||dd}||d}||kstqdS)zS Checks that the root points are sorted in ascending order by y-coordinate N)rangelenAssertionError) root_pointsiZy0Zy1r w/home/dh_an3skk/arjun-chandrasekhar-teaching.com/tomato/backend/backend_plant_architecture/read_arbor_reconstruction.pycheck_root_points s r c Cs|D]}||sttd}d}|d}d}|D]4}t|||rLd}qht||} | |kr2| }|}q2|rnq|dkszt||st|j|ddkst|||rt|||||||d<qdS) aW Method for connecting the start of each lateral root to the closest main root point. G - the network consisting of disconnected main and lateral roots root_points - the (x, y) coordinates for the points on the main root tracing lateral_starts - the (x, y) coordinates for the points at the start of every lateral root infNrFTlabel) main rootmain root baselength) has_noderfloatnxZhas_pathrnodesZhas_edgeadd_edge) Gr lateral_startsZ lateral_startZ closest_distZ closest_pointZ y_lateralZ is_connectedZ root_pointdistr r r connect_lateral_rootss,    rc Csht}|d|jd<d}d}g}g}td|t|f}|D]}|d}|d}t|dkrt|d}d}qBtt t |} |dkr| | s| | |d kr| | n,|| krqB||| t|| ||| d <|d krd |j| d <| | nd |j| d <| }qBW5QRX|d} d |j| d <| |jd <t|||t|t|sdt|S)z Read the arbor reconstruction corresponding to a full arbor tracing. First, this method individually reconstructs the main root and lateral roots separately. Afterwards, each lateral root is connected to the closest main root point .csv arbor nameN%s/%s ,rrrrrz lateral rootr)rGraphstripgraphopenRECONSTRUCTIONS_DIRsplitrtuplemaprradd_nodeappendrrrrZrelabel_lateral_root_tipsZis_treer) fname pathPrefixrZ prev_pointZ curr_rootr rflineZpointZmain_root_baser r r read_arbor_fullMsF           r/cCstjd|t|fdd}|d}|d}|d}|d}t}|d|jd <t||||D]\}} } } | | f} d | f} |d kr|| d |j | d <| |jd <q`|d kr`| | | d|j | d <d|j | d <t | | || | d<q`t ||S)NrT)skipinitialspacez root orderz x coordinatez y coordinatezinsertion pointrrrrrrzlateral root tiprr) pdread_csvr%rr!r"r#zipr)rrrZconnect_main_root)r+r,dfZ root_orderZx_coordZy_coordZinsertion_pointrorderxyZ insertionp1p2r r r read_arbor_condenseds*   r:cCsLtttddtD],}ttdkrtd|krt|t|}qdS)Nr/)oslistdir BASE_PATHrr%rprintr/)arborrr r r mainsrA__main__)ZnetworkxrZscipy.spatial.distancerutils new_constantsr<pandasr1sysrr rr/r:rA__name__r r r r s   :B