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Merge pull request #5 from medtune/dev-0.0.3
Bump v0.0.3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| FROM golang:1.10 | ||
| FROM golang:1.11 | ||
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| # Update system (ubuntu) | ||
| RUN apt-get update && apt update | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,135 @@ | ||
| import tensorflow as tf | ||
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| import DenseNet.preprocessing.densenet_pre as dp | ||
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| import pandas as pd | ||
| import json, codecs | ||
| import os | ||
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| ROLE="chexray preprocessing for densenet 121" | ||
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| flags = tf.app.flags | ||
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| flags.DEFINE_string('data_path', 'data', 'data directory path') | ||
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| # Server flags | ||
| flags.DEFINE_integer('port', 12030, 'flask listen port') | ||
| flags.DEFINE_boolean('debug', False, 'debug flask server') | ||
| FLAGS = flags.FLAGS | ||
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| # Define consts | ||
| base_path = FLAGS.data_path | ||
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| if not os.path.exists(base_path): | ||
| print('creating base path:', base_path) | ||
| os.mkdir(base_path) | ||
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| print("[INFO] initializing tf graph...") | ||
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| # Create main graph | ||
| MainGraph = tf.Graph() | ||
| with MainGraph.as_default(): | ||
| tf.logging.set_verbosity(tf.logging.INFO) | ||
| file_input = tf.placeholder(tf.string, ()) | ||
| image = tf.image.decode_image(tf.read_file(file_input), channels=3) | ||
| copy = tf.identity(image) | ||
| image = tf.image.convert_image_dtype(image, tf.float32) | ||
| image.set_shape([None,None,3]) | ||
| image = dp.preprocess_image(image, 224,224, is_training=False) | ||
| image = tf.expand_dims(image,0) | ||
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| print("[INFO] initialized") | ||
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| # Run cam on image | ||
| def pp_image(graph, src): | ||
| sess = tf.Session(graph=graph) | ||
| img = sess.run([image], {file_input : src}) | ||
| sess.close() | ||
| return img | ||
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| if not os.path.exists(base_path): | ||
| print('creating base path:', base_path) | ||
| os.mkdir(base_path) | ||
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| from flask import ( | ||
| Flask, | ||
| redirect, | ||
| url_for, | ||
| render_template, | ||
| request, | ||
| session, | ||
| ) | ||
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| from flask import ( | ||
| make_response, | ||
| jsonify, | ||
| ) | ||
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| # Flask app | ||
| app = Flask(__name__) | ||
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| # send json response | ||
| def sendJSON(obj): | ||
| return make_response(jsonify(obj)) | ||
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| @app.route('/process', methods=["POST"]) | ||
| def process_image(): | ||
| try: | ||
| target = request.json.get('target') | ||
| targetTemp = target | ||
| target = os.path.join(base_path, target) | ||
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| array = pp_image(MainGraph, target) | ||
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| return sendJSON({ | ||
| 'success' : True, | ||
| 'target' : targetTemp, | ||
| 'out' : pd.Series(array).to_json(orient='values'), | ||
| }), 200 | ||
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| except Exception as e: | ||
| return sendJSON({ | ||
| 'success' : False, | ||
| 'target' : targetTemp, | ||
| 'errors' : [repr(e)], | ||
| }), 200 | ||
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| @app.route('/status', methods=["GET"]) | ||
| def status(): | ||
| return sendJSON({ | ||
| 'success': True, | ||
| 'status' : 'AVAILABLE', | ||
| 'version' : 1, | ||
| 'pwd' : os.getcwd(), | ||
| 'base_path' : base_path, | ||
| 'flask_debug' : FLAGS.debug, | ||
| 'flask_port' : FLAGS.port, | ||
| }), 200 | ||
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| @app.route('/list', methods=["GET"]) | ||
| def get_available_data(): | ||
| try: | ||
| files = [] | ||
| for fname in os.listdir(base_path): | ||
| path = os.path.join(base_path, fname) | ||
| if os.path.isdir(path): | ||
| continue | ||
| files += [path] | ||
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| return sendJSON({ | ||
| 'success' : True, | ||
| 'files' : files, | ||
| }) | ||
| except Exception as e: | ||
| return sendJSON({ | ||
| 'success' : False, | ||
| 'errors' : [repr(e)], | ||
| }), 200 | ||
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| if __name__ == "__main__": | ||
| # Run server | ||
| app.run( | ||
| host='0.0.0.0', | ||
| port=FLAGS.port, | ||
| debug=FLAGS.debug, | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| pandas | ||
| flask |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,119 @@ | ||
| package main | ||
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| import ( | ||
| "bytes" | ||
| "context" | ||
| "encoding/json" | ||
| "fmt" | ||
| "io/ioutil" | ||
| "log" | ||
| "net/http" | ||
| "time" | ||
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| "github.com/medtune/capsul/pkg/pbreq" | ||
| "github.com/medtune/capsul/pkg/pbreq/stdimpl" | ||
| tfsclient "github.com/medtune/capsul/pkg/tfs-client" | ||
| ) | ||
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| type responsePP struct { | ||
| Success bool `json:"success"` | ||
| Target string `json:"target"` | ||
| Out string `json:"out"` | ||
| } | ||
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| type imageData struct { | ||
| data []float64 | ||
| } | ||
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| type requestPP struct { | ||
| Target string `json:"target"` | ||
| } | ||
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| func getFloatList(file string) (*responsePP, error) { | ||
| url := "http://localhost:12030/process" | ||
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| jsonStr, err := json.Marshal(&requestPP{file}) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
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| req, err := http.NewRequest("POST", url, bytes.NewBuffer(jsonStr)) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
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| req.Header.Set("Content-Type", "application/json") | ||
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| client := &http.Client{} | ||
| r, err := client.Do(req) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
| defer r.Body.Close() | ||
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| body, err := ioutil.ReadAll(r.Body) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
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| t := responsePP{} | ||
| err = json.Unmarshal(body, &t) | ||
| if err != nil { | ||
| return nil, err | ||
| } | ||
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| return &t, nil | ||
| } | ||
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| func main() { | ||
| start := time.Now() | ||
| // Read image file | ||
| r, err := getFloatList("00000003_002.png") | ||
| if err != nil { | ||
| log.Fatalln(err) | ||
| } | ||
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| var data [][][][][]float32 | ||
| err = json.Unmarshal([]byte(r.Out), &data) | ||
| if err != nil { | ||
| log.Fatalln(err) | ||
| } | ||
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| var onelist []float32 | ||
| d := data[0][0] | ||
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| for _, i := range d { | ||
| for _, j := range i { | ||
| onelist = append(onelist, j[0], j[1], j[2]) | ||
| } | ||
| } | ||
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| fmt.Println(len(onelist)) | ||
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| // Connection to tf server | ||
| client, err := tfsclient.New("localhost:10031") | ||
| if err != nil { | ||
| panic(err) | ||
| } | ||
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| // timeout context | ||
| ctx, cancel := context.WithTimeout(context.Background(), 10*time.Second) | ||
| defer cancel() | ||
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| // Prediction Request: | ||
| meta := stdimpl.ChexrayDN121 | ||
| req := pbreq.PredictFTest(meta, onelist) | ||
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| // Run prediction | ||
| resp, err := client.Predict(ctx, req) | ||
| if err != nil { | ||
| panic(err) | ||
| } | ||
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| l := resp.GetOutputs()["scores"].GetFloatVal() | ||
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| for _, i := range l { | ||
| fmt.Printf("%.2f ", i*float32(100)) | ||
| } | ||
| fmt.Println(time.Since(start)) | ||
| } |
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