CN104504682A - Animal shape phenotype automatic measuring method - Google Patents
Animal shape phenotype automatic measuring method Download PDFInfo
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Abstract
Disclosed is an animal shape phenotype automatic measuring method. An animal shape phenotype is automatically measured through template deformation. The method comprises the following steps: establishing a database, i.e., establishing a template model database storing three-dimensional stereo templates of different animals in different growth periods, and a shape phenotype measuring definition database storing shape phenotype index measuring definitions measuring different animal shape phenotype indexes; coupling, i.e., according to the three-dimensional stereo templates in the template model database, comparing input animal data models, obtaining three-dimensional stereo templates which are closest to the types of the currently input animal data models and the growth periods as the coupling templates of the currently input animal data templates; deformation, i.e., according to the input animal data models, deforming the coupling templates until the coupling templates are close to the currently input animal data models in terms of body size; and calculating, i.e., according to the shape phenotype measuring definitions in the shape phenotype measuring definition database and the deformed coupling templates, obtaining the shape phenotype indexes of the input animal data models. The animal shape phenotype automatic measuring method improves the automation degree of animal shape phenotype measurement.
Description
Technical field
The present invention relates to three-dimensional (3D) computer vision field, particularly relate to a kind of animals shaped phenotype method for automatic measurement based on template deformation.
Background technology
In agricultural production link, breeding, body weight estimation and body measurement etc. are comprised to the application of the animals shaped phenotypes such as horse cattle and sheep pig.These application all relate to the various indexs measuring animals shaped phenotype, but the various data processing work amount that causes of required various evaluation index quantity is large.Therefore, full-automatic high flux acquisition animal 3D shape phenotypic correlation index has certain production meaning.
In current actual production, most is that the measurers such as manual application graphometer, slide calliper rule, tape measure carry out measuring or directly observing marking by expert.The acquisition of evaluation index data is by manually completing, and workload is very big.In current semi-automatic solution, the design that majority utilizes image processing techniques to carry out animal build assessment system hardware and software, realizes the measurement to kinetoplast type form parameter.But image processing techniques requires strict for the pose of animal, otherwise larger error will be caused to occur, thus practicality is strong, is main measurement means in actual production or with human expert marking.The equipment patent abroad estimated animal build is more, if publication number is the patent of US8036429, US7214128, US6860226 respectively.The above-mentioned equipment carrying out estimating is measure the build position of animal, the device of project organization, in conjunction with multiple image acquisition and sonar sensor, and then obtains the build of animal and the measurement parameter of bone.But this kind of method not only higher system complex of cost, resets repacking for adapting to different animals needs to one-piece construction simultaneously.
Current robotization index selection method mainly realizes based on the pose of two dimensional image and structural devices restriction animal.For animal pose or to gather environmental requirement comparatively strict, be difficult to meet under particularly domestic actual production environment.So in current practical application or based on expert's manual observation test and appraisal, and two dimensional image technology itself can not obtain the index relevant to animal bodies curve form.
Summary of the invention
The technical problem to be solved in the present invention is to provide one and measures accurate, system simplification, the animals shaped phenotype method for automatic measurement based on template deformation of high flux, low cost.
In order to solve the problems of the technologies described above, the invention provides a kind of animals shaped phenotype method for automatic measurement.This measuring method comprises the following steps:
Build storehouse, set up the template model database of the 3 D stereo template storing different animals different growing stages, and the shape phenotype storing the shape phenotype index measurement definition of measuring different animals shape phenotype index measures definition database;
Coupling, according to the 3 D stereo template in described template model database, the animal data model of comparison input, obtain with the animal data version of current input, growth period immediate 3 D stereo template as the matching template of the described animal data model of current input;
Distortion, according to the described animal data model of input, carries out the described animal data model body size be deformed into current input and is close by described matching template;
Calculate, the matching template after measuring definition and distortion according to the described shape phenotype in described shape phenotype measurement definition database carries out numerical evaluation, obtains the shape phenotype index of the described animal data model inputted.
Preferably, described in build in the step of storehouse, it is corresponding with each 3 D stereo template in described template model database that the described shape phenotype that described shape phenotype index measurement definition database stores measures definition.
Preferably, described shape phenotype measurement definition comprises: the title of shape phenotype index, the biological marker point of described shape phenotype index, and the computing method of described shape phenotype index.
Preferably, described computing method are the air line distance between described biological marker point, the distance on projecting direction, geodesic line distance; Or any spacing, the geodesic line Distance geometry of multiple labeling point.
Preferably, in described coupling step, the described animal data model of current input is some cloud after three-dimensional reconstruction or grid data model.
Preferably, in described deforming step, according to the described animal data model of input, adopt Laplce's distortion that described matching template is carried out the described animal data model body size be deformed into current input and be close.
Preferably, also comprise step described building between storehouse step and described coupling step: input, inputs current animal data model, and read in it and resolve.
Technique scheme tool of the present invention has the following advantages: animals shaped phenotype method for automatic measurement provided by the invention is by the application of database and template deformation technology, and the template data in conjunction with different animals realizes carrying out all automatic measurement to animals shaped phenotype predefine index.Avoid transmission and in the measurements height is required to pose based on the technical scheme of two dimensional image and to shortcomings such as collection environmental requirement are high, by the treatment channel being data source with the some cloud after animal three-dimensional reconstruction or grid model.Improve versatility, flexibly fixed and automaticity.
Accompanying drawing explanation
Fig. 1 is the method step process flow diagram of the animals shaped phenotype method for automatic measurement that the embodiment of the present invention provides;
Fig. 2 is the specific works flow process figure of the animals shaped phenotype method for automatic measurement that the embodiment of the present invention provides;
Fig. 3 (a), Fig. 3 (b), Fig. 3 (c), Fig. 3 (d) are rear view, side view, vertical view, the 3D view of the 3D shape template of the animals shaped phenotype method for automatic measurement animal A that the embodiment of the present invention provides;
Fig. 4 (a), Fig. 4 (b), Fig. 4 (c), Fig. 4 (d) are rear view, side view, vertical view, the 3D view of the some cloud template after the three-dimensional reconstruction of the animals shaped phenotype method for automatic measurement animal A that the embodiment of the present invention provides;
Fig. 5 (a), Fig. 5 (b), Fig. 5 (c), Fig. 5 (d) are rear view, side view, vertical view, the 3D view of the distortion rear pattern plate of the animals shaped phenotype method for automatic measurement animal A that the embodiment of the present invention provides.
Embodiment
Below in conjunction with drawings and Examples, the specific embodiment of the present invention is described in further detail.Following examples for illustration of the present invention, but are not used for limiting the scope of the invention.
Along with the development of science and technology, three-dimensional reconstruction and points cloud processing technology comparatively universal, existing laser or other clouds obtain equipment and also can be used for build measuring technique.In recent years, the structure luminous point cloud of low cost obtains the universal of equipment, makes to obtain animal 3D point cloud or grid data model is comparatively easy and cost is lower.Animals shaped phenotype method for automatic measurement provided by the invention, realizes carrying out all automatic measurement to animals shaped phenotype predefine index in conjunction with the application of template deformation technology for input with the animal 3D point cloud after three-dimensional reconstruction or network data model.
As shown in Figure 1, the method step process flow diagram of the animals shaped phenotype method for automatic measurement provided for the embodiment of the present invention.
Embodiments provide a kind of animals shaped phenotype method for automatic measurement, this measuring method comprises: build storehouse, set up the template model database of the 3 D stereo template storing different animals different growing stages, and store the shape phenotype index measurement definition database of the shape phenotype index measurement definition of measuring different animals shape phenotype index; Coupling, according to the 3 D stereo template in template model database, the animal data model of comparison input, obtain with the animal data version of current input, growth period immediate 3 D stereo template as the matching template of the animal data model of current input; Distortion, according to the animal data model of input, carries out the animal data model body size be deformed into current input and is close by matching template; Calculate, the matching template after measuring definition and distortion according to the shape phenotype in shape phenotype measurement definition database carries out numerical evaluation, obtains the shape phenotype index of the animal data model inputted.
Further, in the step of building storehouse, it is corresponding with 3 D stereo template each in template model database that the shape phenotype that shape phenotype index measurement definition database stores measures definition.Wherein, shape phenotype measurement definition comprises: the title of shape phenotype index, the biological marker point of shape phenotype index, and the computing method of shape phenotype index.Computing method are the air line distance between biology gauge point, the distance on projecting direction, geodesic line distance; Or any spacing, the geodesic line Distance geometry of multiple labeling point.
Further, in the step of coupling, the animal data model of current input is some cloud after three-dimensional reconstruction or grid data model.Wherein, comprise owing to certainly blocking the small holes caused in cloud data or grid data.
Further, in the step of distortion, adopt Laplce's distortion to be out of shape by matching template, but not as limit, animals shapedly can adopt deformation method flexibly according to different.Make it the matching template after being out of shape closest to the body size of the animal data model of current input, and then can reach and exactly, automatically animals shaped phenotype is measured.
Further, also step is comprised building between the step in storehouse and the step of coupling: input, inputs current animal data model, and read in it and resolve.
Further, as shown in Figure 2, the specific works flow process figure of animals shaped phenotype automatic measurement system that provides of the embodiment of the present invention.When carrying out implementation and operation, perform step S0: off-line sets up template model database and shape phenotype index measurement definition database.Suppose the related data of at least preserving animal species A in template model database, namely also attach the parameters such as the length and width height of animal A from birth to natural death every the 3D shape template data of the normal type of 1 month.Wherein, in the present embodiment, animal species A is for pig, and the 3D shape template data instance of pig is as shown in Fig. 3 (a), Fig. 3 (b), Fig. 3 (c), Fig. 3 (d).Shape phenotype index measurement definition database is preserved the shape phenotype corresponding to each template in template model database and is measured definition.Wherein, shape phenotype is measured definition and is comprised shape phenotype index name, and the biological marker point of shape phenotype index, and the computing method etc. of shape phenotype index.
Further, the computing method of shape phenotype index can be air line distance, the distance on a certain projecting direction, geodesic line Distance geometry between 2 biological marker points, or air line distance, the geodesic line Distance geometry of User Defined multiple labeling point composition free routing.In the present embodiment, the shape phenotype index measurement database instance of pig is as shown in table 1.In the present embodiment pig shape phenotype index measurement definition database in preserve: shape phenotype index name is that body is long, corresponding biological marker point P1, P2, the vertical view of the 3D shape template of composition graphs 3 (c) pig, its computing method are the projector distance on the length direction of pig; Shape phenotype index name is that body is wide, corresponding biological marker point P3, P4, the vertical view of the 3D shape template of composition graphs 3 (c) pig, and its computing method are the projector distance on the Width of pig; Shape phenotype index name is height, corresponding biological marker point P5, P6, the side view of the 3D shape template of composition graphs 3 (b) pig, and its computing method are the projector distance in the short transverse of pig; Shape phenotype index name be self-defined name as lower limb and upper height, corresponding biological marker point P7, P8, P9, P10, the rear view of the 3D shape template of composition graphs 3 (a) pig, its computing method are four gauge point geodesic lines distance sums.
The shape phenotype index measurement definition database example of table 1 pig
| Shape phenotype index name | Biomarkers point | Computing method |
| Body is long | P1，P2 | Length direction projector distance |
| Body is wide | P3，P4 | Width projector distance |
| Height | P5，P6 | Short transverse projector distance |
| Self-defined | P7，P8，P9，P10 | Each gauge point geodesic line Distance geometry |
Further, perform step S1: user is some cloud after the three-dimensional reconstruction of the random individual of pig or grid data model by input style, obtains the cloud data model after the three-dimensional reconstruction of pig as shown in Fig. 4 (a), Fig. 4 (b), Fig. 4 (c), Fig. 4 (d).And then the shape phenotype index that execution step S2-S7 carries out pig is measured automatically, and concrete steps are:
Step S2: first, user take kind as some cloud after the three-dimensional reconstruction of the random individual 01 of pig or grid data model is input data, and the cloud data model instance after the three-dimensional reconstruction of pig is as shown in Fig. 4 (a), Fig. 4 (b), Fig. 4 (c), Fig. 4 (d).Input data to animal data mode input subsystem, reading in and parsing of the complete paired data of this subsystem, and save as the some cloud after three-dimensional reconstruction or network data model, the animal data model Data_A_01 of current input.
Step S3: start matching parameter extraction module, this module for input, exports the length, width and height parameter Signature_A_01 of the random individual 01 of corresponding pig with the animal data model Data_A_01 of current input.
Step S4: carry out template matches, starts template matches module.This module is with length, width and height parameter Signature_A_01 for input, and connection mode Slab database, carries out retrieval contrast.Obtaining the template data minimum with length, width and height parameter Signature_A_01 parameter value error, is matching template Index_Model_A_01.Meanwhile, obtain the shape phenotype corresponding with the length, width and height parameter Signature_A_01 inputted and measure that to define Index_Rules_A_01 as shown in table 1.
Step S5: start template deformation subsystem, this subsystem with the animal data model Data_A_01 of matching template Index_Model_A_01 and current input for input, utilize the deformation method based on Laplacian algorithm, obtain the template Model_Deformed_A_01 after being out of shape, make the template Model_Deformed_A_01 after distortion close to the body size of the animal data model Data_A_01 of current input, and then can reach and exactly, automatically measure animals shaped phenotype.As shown in Fig. 5 (a), Fig. 5 (b), Fig. 5 (c), Fig. 5 (d).
Step S6: start shape phenotype index calculate and report output subsystem, this subsystem is connected with shape phenotype index measurement definition database, measure definition Index_Rules_A_01 for input with the template Model_Deformed_A_01 after distortion and shape phenotype, carry out the calculating of corresponding shape phenotype index according to the definition of shape phenotype index measurement.
Step S7: export the shape phenotype index measurement result form that animal species is pig individuality 01 to user, as shown in table 2.Animal species is the random individual 01 of pig, the measurement of shape phenotype was carried out on October 12 at 201*, the shape phenotype index measurement database used and the version of template model database are * .0 version, the deformation method used is out of shape for Laplce, the shape phenotype index obtained is respectively: the long 984.20mm of body, the wide 316.44mm of body, height 660.21mm, self-defining lower limb and upper height 420.31mm.
The shape phenotype index measurement result form of table 2 pig
| Animal species title | Pig |
| Number of animals | 01 |
| Measure the date | 201* October 12 |
| The shape phenotype index measurement definition database version used | *.0 |
| The template model database version used | *.0 |
| The deformation method used | Laplce is out of shape |
| Survey shape phenotype index name | Measured value (mm) |
| Body is long | 984.20 |
| Body is wide | 316.44 |
| Height | 660.21 |
| Self-defined | 420.31 |
Animal species in the present embodiment is for pig, but not as limit, all available animals shaped phenotype method for automatic measurement provided by the invention of animal such as other animals such as ox, horse, sheep carry out all automatic measurement to its shape phenotype.
In sum, animals shaped phenotype automatic measurement system provided by the invention is by the application of database and template deformation technology, and the template data in conjunction with different animals realizes carrying out all automatic measurement to animals shaped phenotype predefine index.Avoid transmission and in the measurements height is required to pose based on the technical scheme of two dimensional image and to shortcomings such as collection environmental requirement are high, by the treatment channel being data source with the some cloud after animal three-dimensional reconstruction or grid model.Improve versatility, flexibly fixed and automaticity.
Last it is noted that above embodiment is only in order to illustrate technical scheme of the present invention, be not intended to limit; Although with reference to previous embodiment to invention has been detailed description, those of ordinary skill in the art is to be understood that: it still can be modified to the technical scheme described in foregoing embodiments, or carries out equivalent replacement to wherein portion of techniques feature; And these amendments or replacement, do not make the essence of appropriate technical solution depart from the spirit and scope of various embodiments of the present invention technical scheme.
Claims (7)
1. an animals shaped phenotype method for automatic measurement, is characterized in that, comprise the following steps:
Build storehouse, set up the template model database of the 3 D stereo template storing different animals different growing stages, and the shape phenotype storing the shape phenotype index measurement definition of measuring different animals shape phenotype index measures definition database;
Coupling, according to the 3 D stereo template in described template model database, the animal data model of comparison input, obtain with the animal data version of current input, growth period immediate 3 D stereo template as the matching template of the described animal data model of current input;
Distortion, according to the described animal data model of input, carries out the described animal data model body size be deformed into current input and is close by described matching template;
Calculate, the matching template after measuring definition and distortion according to the described shape phenotype in described shape phenotype measurement definition database carries out numerical evaluation, obtains the shape phenotype index of the described animal data model inputted.
2. animals shaped phenotype method for automatic measurement according to claim 1, it is characterized in that, describedly build in the step of storehouse, it is corresponding with each 3 D stereo template in described template model database that the described shape phenotype that described shape phenotype index measurement definition database stores measures definition.
3. animals shaped phenotype method for automatic measurement according to claim 2, it is characterized in that, described shape phenotype is measured definition and is comprised: the title of shape phenotype index, the biological marker point of described shape phenotype index, and the computing method of described shape phenotype index.
4. animals shaped phenotype method for automatic measurement according to claim 3, is characterized in that, described computing method are the air line distance between described biological marker point, the distance on projecting direction, geodesic line distance; Or any spacing, the geodesic line Distance geometry of multiple labeling point.
5. the animals shaped phenotype method for automatic measurement according to any one of claim 1-4, is characterized in that, in described coupling step, the described animal data model of current input is some cloud after three-dimensional reconstruction or grid data model.
6. animals shaped phenotype method for automatic measurement according to claim 5, it is characterized in that, in described deforming step, according to the described animal data model of input, adopt Laplce's distortion that described matching template is carried out the described animal data model body size be deformed into current input and be close.
7. animals shaped phenotype method for automatic measurement according to claim 6, is characterized in that, also comprises step described building between storehouse step and described coupling step: input, inputs current animal data model, and read in it and resolve.
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