Merge pull request #12 from ideaconsult/updates_pyambit

Updates pyambit

pyproject.toml

@@ -47,6 +47,7 @@ requests = "^2.31.0"
 xlsxwriter = "^3.1.9"
 measurement = "^3.2.2"
 openpyxl = "^3.1.2"
+pyambit = {git = "https://github.com/ideaconsult/pyambit.git"}
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/ideaconsult/pynanomapper/issues"

src/pynanomapper/aa.py

@@ -40,7 +40,8 @@ def __init__(self, token=None):
         self.token = token
 
     def __call__(self, r):
-        r.headers['Authorization'] = "Bearer {}".format(self.token)
+        if self.token != None:
+            r.headers['Authorization'] = "Bearer {}".format(self.token)
         return r
 
     def setKey(self, token):

src/pynanomapper/clients/authservice.py

@@ -43,7 +43,9 @@ def logout(self):
     def getHeaders(self):
         headers = {}
         headers["Accept"] = "application/json"
-        headers["Authorization"] = "Bearer {}".format(self.token['access_token'])
+        _token = self.token['access_token']
+        if _token != None:
+            headers["Authorization"] = "Bearer {}".format(_token)
         return headers
 
 

src/pynanomapper/clients/datamodel_simple.py

@@ -34,8 +34,8 @@ def __init__(self, investigation, provider, parameters, filename, spectrum_embed
         self.spectrum_embedding = spectrum_embedding
 
     @staticmethod
-    def x4search():
-        return np.linspace(140,3*1024+140,num=1024)
+    def x4search(dim=1024):
+        return np.linspace(140,3*1024+140,num=dim)
         #return np.linspace(140,140+2048,num=1024)
 
     @staticmethod
@@ -79,16 +79,16 @@ def xy2embedding(x,y,xlinspace = None,remove_baseline=True,window=16):
         if xlinspace is None:
             xlinspace = StudyRaman.x4search()
         spe = rc2.spectrum.Spectrum(x=x, y=y, metadata={})
-        (spe,hist_dist,index) = StudyRaman.spectra2dist(spe,xcrop = [xlinspace[0],xlinspace[-1]],remove_baseline=True,window=window)
+        (spe,hist_dist,index) = StudyRaman.spectra2dist(spe,xcrop = [xlinspace[0],xlinspace[-1]],remove_baseline=remove_baseline,window=window)
         return (hist_dist.cdf(xlinspace),hist_dist.pdf(xlinspace))
 
     @staticmethod
-    def h52embedding(h5,dataset="raw",xlinspace = None):
+    def h52embedding(h5,dataset="raw",xlinspace = None,remove_baseline=True,window=16):
         if xlinspace is None:
             xlinspace = StudyRaman.x4search()
         x = h5[dataset][0]
         y = h5[dataset][1]
-        return StudyRaman.xy2embedding(x,y,xlinspace)
+        return StudyRaman.xy2embedding(x,y,xlinspace,remove_baseline=remove_baseline,window=window)
 
     def to_solr_json(self):
         _solr = {}

src/pynanomapper/clients/service_charisma.py

@@ -135,12 +135,16 @@ def dict2figure(pm,figsize):
 
     def solrquery_get(self,solr_url, params):
         headers = {}
-        headers["Authorization"] = "Bearer {}".format(self.tokenservice.api_key());
+        _token = self.tokenservice.api_key()
+        if _token != None:
+            headers["Authorization"] = "Bearer {}".format(_token);
         return requests.get(solr_url, params = params, headers= headers)
 
     def solrquery_post(self,solr_url, json):
         headers = {}
-        headers["Authorization"] = "Bearer {}".format(self.tokenservice.api_key());
+        _token = self.tokenservice.api_key()
+        if _token != None:
+            headers["Authorization"] = "Bearer {}".format(_token);
         return requests.get(solr_url, json = json, headers= headers)
 
     def thumbnail(self,solr_url,domain,figsize=(6,4),extraprm=""):
@@ -197,14 +201,15 @@ def image(self,domain,dataset="raw",figsize=(6,4),extraprm=""):
         except Exception as err:
             return self.empty_figure(figsize,"Error","{}".format(domain.split("/")[-1]))
 
-    def knnquery(self,domain,dataset="raw"):
+    def knnquery(self,domain,dataset="raw",dim=1024):
         try:
             with self.File(domain,mode="r") as h5:
                 x = h5[dataset][0]
                 y = h5[dataset][1]
-                (cdf,pdf) = StudyRaman.h52embedding(h5,dataset="raw",xlinspace = StudyRaman.x4search())
+                (cdf,pdf) = StudyRaman.h52embedding(h5,dataset="raw",xlinspace = StudyRaman.x4search(dim=dim))
                 result_json = {}
-                result_json["cdf"] = compress(cdf.tolist(),precision=6)
+                result_json["cdf"] = compress(cdf.tolist(),precision=4)
+                result_json["pdf"] = compress(pdf.tolist(),precision=4)
                 #return ','.join(map(str, cdf))
                 try:
                     px = 1/plt.rcParams['figure.dpi']  # pixel in inches