lunapi 0.1.1__cp310-cp310-macosx_10_9_x86_64.whl → 1.2.0__cp310-cp310-macosx_10_9_x86_64.whl

lunapi/lunapi0.cpp

@@ -66,7 +66,9 @@ PYBIND11_MODULE(lunapi0, m) {
     .def( "get_sample_list" ,
           &lunapi_t::sample_list,
           "Return the loaded sample list" )
-    
+    .def( "validate_sample_list" , 
+	  &lunapi_t::validate_sample_list ,
+	  "Validate an attached sample list" )
     .def( "insert_inst" , &lunapi_t::insert_inst )
     .def( "nobs" , &lunapi_t::nobs )
     .def( "clear" , &lunapi_t::clear )
@@ -112,8 +114,13 @@ PYBIND11_MODULE(lunapi0, m) {
     .def( "inst" ,
 	  py::overload_cast<const std::string&>
 	  (&lunapi_t::inst,py::const_),
-	  "Generate an empty lunapi-instance" )
+	  "Generate an lunapi-instance" )
     
+    .def( "empty_inst" ,
+	  py::overload_cast<const std::string&,const int, const int, const std::string&, const std::string&>
+	  (&lunapi_t::inst,py::const_),
+	  "Generate an empty lunapi-instance of fixed record size" )
+
     .def( "inst" ,
 	  py::overload_cast<const std::string&,const std::string &>
 	  (&lunapi_t::inst,py::const_),

lunapi/lunapi1.py

@@ -1,7 +1,7 @@
 """lunapi1 module: a high-level wrapper around lunapi0 module functions"""
 
 # Luna Python interface (lunapi)
-# v0.1.1, 30-May-2024
+# v0.1.2, 17-Dec-2024
 
 import lunapi.lunapi0 as _luna
 
@@ -33,7 +33,7 @@ class resources:
    POPS_LIB = 's2'
    MODEL_PATH = '/build/luna-models/'
 
-lp_version = "v0.1.1"
+lp_version = "v0.1.2"
    
 # C++ singleton class (engine & sample list)
 # lunapi_t      --> luna
@@ -83,7 +83,11 @@ class proj:
           a list of folder names and optional arguments to be passed to build
 
       """
-          
+
+      # first clear any existing sample list
+      proj.eng.clear()
+
+      # then try to build a new one
       if type( args ) is not list: args = [ args ]
       return proj.eng.build_sample_list( args )
 
@@ -144,6 +148,28 @@ class proj:
 
       return proj.eng.nobs()
 
+   #------------------------------------------------------------------------
+      
+   def validate( self ):
+      """Validates an internal sample-list 
+      
+      This provides the same functionality
+      as the `--validate` option of Luna, which is described here:
+
+      https://zzz.bwh.harvard.edu/luna/ref/helpers/#-validate
+
+      Parameters
+      ----------
+      none
+
+      """
+
+      tbl = proj.eng.validate_sample_list()
+      tbl = pd.DataFrame( tbl )
+      tbl.columns = [ 'ID' , 'Filename', 'Valid' ]
+      tbl.index += 1
+      return tbl
+
 
    #------------------------------------------------------------------------
       
@@ -173,6 +199,24 @@ class proj:
       return inst(proj.eng.inst( n ))
       
 
+   #------------------------------------------------------------------------
+   
+   def empty_inst( self, id, nr, rs, startdate = '01.01.00', starttime = '00.00.00' ):
+      """Generates a new instance with empty fixed-size EDF"""
+
+      # check inputs
+      nr = int( nr )
+      rs = int( rs )
+      if nr < 0:
+         print( "expecting nr (number of records) to be a positive integer" )
+         return      
+      if rs < 0:
+         print( "expecting rs (record duration, secs) to be a positive integer" )
+         return
+      
+      # return instance of fixed size
+      return inst(proj.eng.empty_inst(id, nr, rs, startdate, starttime ))
+
    #------------------------------------------------------------------------
    def clear(self):
       """Clears any existing project sample-list"""
@@ -798,40 +842,6 @@ class inst:
       #df = df.drop(columns = ['ID','TP','MID','INTERVAL'] )
       return df
       
-   # --------------------------------------------------------------------------------
-   def psd( self, ch, var = 'PSD' , minf = None, maxf = None, minp = None, maxp = None , xlines = None , ylines = None ):
-      """Generates a PSD plot (from PSD or MTM)"""
-      if ch is None: return
-      if type(ch) is not list: ch = [ ch ]
-
-      if var == 'PSD':
-         self.eval( 'PSD spectrum dB sig=' + ','.join(ch) )
-         df = self.table( 'PSD' , 'CH_F' )
-      else:
-         self.eval( 'MTM tw=15 dB sig=' + ','.join(ch) )
-         df = self.table( 'MTM' , 'CH_F' )
-         
-      psd( df = df , ch = ch , var = var ,
-           minf = minf , maxf = maxf , minp = minp , maxp = maxp ,
-           xlines = xlines , ylines = ylines )
-      
-    
-   # --------------------------------------------------------------------------------
-   def spec( self, ch, var = 'PSD' , mine = None, maxe = None, minf = None, maxf = None , w = 0.025 ):
-      """Generates an epoch-level PSD spectrogram (from PSD or MTM)"""
-      if ch is None: return
-      if type(ch) is not list: ch = [ ch ]
-
-      if var == 'PSD':
-         self.eval( 'PSD epoch-spectrum dB sig=' + ','.join(ch) )
-         df = self.table( 'PSD' , 'CH_E_F' )
-      else:
-         self.eval( 'MTM epoch-spectra epoch epoch-output dB tw=15 sig=' + ','.join(ch) )
-         df = self.table( 'MTM' , 'CH_E_F' )
-         
-      spec( df = df , ch = None , var = var ,
-            mine = mine , maxe = maxe , minf = minf , maxf = maxf , w = w )
-
 
    # --------------------------------------------------------------------------------
    #  tfview : spectral regional viewer
@@ -1119,7 +1129,49 @@ class inst:
       if type(ch) is not list: ch = [ ch ]
       return self.edf.has_channels( ch )
 
-   # --------------------------------------------------------------------------------                                                                  
+   # --------------------------------------------------------------------------------
+#   def psd(self, ch, minf = None, maxf = 25, minp = None, maxp = None , xlines = None , ylines = None ):
+#      """Spectrogram plot for a given channel 'ch'"""
+#      if type( ch ) is not str: return
+#      if all( self.has( ch ) ) is not True: return
+#      res = self.silent_proc( 'PSD spectrum dB max=' + str(maxf) + ' sig=' + ','.join(ch) )[ 'PSD: CH_F' ]
+#      return psd( res , ch, minf = minf, maxf = maxf, minp = minp, maxp = maxp , xlines = xlines , ylines = ylines )
+
+   # --------------------------------------------------------------------------------
+   def psd( self, ch, var = 'PSD' , minf = None, maxf = 25, minp = None, maxp = None , xlines = None , ylines = None ):
+      """Generates a PSD plot (from PSD or MTM) for one or more channel(s)"""
+      if ch is None: return
+      if type(ch) is not list: ch = [ ch ]
+
+      if var == 'PSD':
+         res = self.silent_proc( 'PSD spectrum dB max=' + str(maxf) + ' sig=' + ','.join(ch) )
+         df = res[ 'PSD: CH_F' ]
+      else:
+         res = self.silent_proc( 'MTM tw=15 dB max=' + str(maxf) + ' sig=' + ','.join(ch) )
+         df = res[ 'MTM: CH_F' ]
+         
+      psd( df = df , ch = ch , var = var ,
+           minf = minf , maxf = maxf , minp = minp , maxp = maxp ,
+           xlines = xlines , ylines = ylines )
+      
+    
+   # --------------------------------------------------------------------------------
+#   def spec( self, ch, var = 'PSD' , mine = None, maxe = None, minf = None, maxf = 25 , w = 0.025 ):
+#      """Generates an epoch-level PSD spectrogram (from PSD or MTM)"""
+#      if ch is None: return
+#      if type(ch) is not list: ch = [ ch ]
+#
+#      if var == 'PSD':
+#         self.eval( 'PSD epoch-spectrum dB max=' + str(maxf) + ' sig=' + ','.join(ch) )
+#         df = self.table( 'PSD' , 'CH_E_F' )
+#      else:
+#         self.eval( 'MTM epoch-spectra epoch epoch-output dB tw=15 max=' + str(maxf) + ' sig=' + ','.join(ch) )
+#         df = self.table( 'MTM' , 'CH_E_F' )
+#         
+#      spec( df = df , ch = None , var = var ,
+#            mine = mine , maxe = maxe , minf = minf , maxf = maxf , w = w )
+
+   # --------------------------------------------------------------------------------
    def spec(self,ch,mine = None , maxe = None , minf = None, maxf = None, w = 0.025 ):
       """PSD given channel 'ch'"""
       if type( ch ) is not str:
@@ -1129,15 +1181,6 @@ class inst:
       res = self.silent_proc( "PSD epoch-spectrum dB sig="+ch )[ 'PSD: CH_E_F' ]
       return spec( res , ch=ch, var='PSD', mine=mine,maxe=maxe,minf=minf,maxf=maxf,w=w)
 
-   # --------------------------------------------------------------------------------
-   def psd(self, ch, minf = None, maxf = None, minp = None, maxp = None , xlines = None , ylines = None ):
-      """Spectrogram plot for a given channel 'ch'"""
-      if type( ch ) is not str:
-         return
-      if all( self.has( ch ) ) is not True:
-         return
-      res = self.silent_proc( "PSD spectrum dB sig="+ch )[ 'PSD: CH_F' ]
-      return psd( res , ch, minf = minf, maxf = maxf, minp = minp, maxp = maxp , xlines = xlines , ylines = ylines )
 
       
 # --------------------------------------------------------------------------------
@@ -2140,12 +2183,12 @@ def scope( p,
         if band_hjorth_sel.value is True:
            S = np.transpose( ss.get_hjorths( pow_sel.value ) )
            S = np.asarray(S,dtype=object)
-           S[np.isnan(S.astype(np.float_))] = None
+           S[np.isnan(S.astype(np.float64))] = None
            bg.update_traces({'z': S } , selector = {'type':'heatmap'} )
         else:
            S = np.transpose( ss.get_bands( pow_sel.value ) )
            S = np.asarray(S,dtype=object)
-           S[np.isnan(S.astype(np.float_))] = None
+           S[np.isnan(S.astype(np.float64))] = None
            bg.update_traces({'z': S } , selector = {'type':'heatmap'} )
 
     def pop_a1(change):
@@ -2276,6 +2319,10 @@ def scope( p,
     update_bandpower(None)
     ss.set_scaling( len(chbox.value) , len( anbox.value) , 2**float(yscale.value) , float(yspace.value) , header_height, footer_height , annot_height )
 
+    ss.window( 0 , 30 )
+    epoch.value = str(1);
+
+    redraw()
     return container_app
 
 
@@ -2293,7 +2340,7 @@ class moonbeam:
       """ Initiate Moonbeam with an NSRR token """
       self.nsrr_tok = nsrr_tok
       self.df1 = self.cohorts()
-      if cdir is None: cdir = os.path.join( tempfile.gettempdir() , 'luna-mmonbeam' )
+      if cdir is None: cdir = os.path.join( tempfile.gettempdir() , 'luna-moonbeam' )
       self.set_cache(cdir)
 
    def set_cache(self,cdir):
@@ -2330,21 +2377,20 @@ class moonbeam:
       return self.df2
 
    
-   def inst(self, iid, cohort = None ):
-      """ Create an instance of a record, either downloaded or cached """    
+   def inst(self, iid ):
+      """ Create an instance of a record, either downloaded or cached """
       if self.df2 is None: return
       if self.curr_cohort is None: return
       
       # ensure we have this file 
-      self.pull( iid , cohort )
+      self.pull( iid , self.curr_cohort )
 
-      # initiate an instance (from singleton proj)
-      proj1 = proj()
+      # ensure we have a proj (from proj singleton)
+      proj1 = proj(False)
       p = proj1.inst( self.curr_id )
-
       edf1 = str( pathlib.Path( self.cdir ).joinpath( self.curr_edf ).expanduser().resolve() )      
       p.attach_edf( edf1 ) 
-
+      
       if self.curr_annot is not None:
          annot1 = str( pathlib.Path( self.cdir ).joinpath( self.curr_annot ).expanduser().resolve() )
          p.attach_annot( annot1 )
@@ -2353,10 +2399,8 @@ class moonbeam:
       return p
 
     
-   def pull(self, iid , cohort = None ):
-      """ Download an individual record (if not already cached) """    
-      if cohort is None and self.df2.empty: return False
-      if self.df2.empty: files( cohort )
+   def pull(self, iid , cohort ):
+      """ Download an individual record (if not already cached) """      
       if self.df2.empty: return False
 
       # iid

{lunapi-0.1.1.dist-info → lunapi-1.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lunapi
-Version: 0.1.1
+Version: 1.2.0
 Summary: Python interface to the Luna toolset for sleep signal analysis
 Keywords: Sleep,EEG,PSG,Luna,Signal processing
 Author-Email: Shaun Purcell <smpurcell@bwh.harvard.edu>, Senthil Palanivelu <spalanivelu@mgh.harvard.edu>, Nataliia Kozhemiako <nkozhemiako@bwh.harvard.edu>
@@ -20,13 +20,15 @@ Classifier: Programming Language :: Python :: 3.13
 Project-URL: Www, https://zzz.bwh.harvard.edu/luna
 Project-URL: Github, http://github.com/remnrem/luna-api
 Requires-Python: >=3.9
-Requires-Dist: matplotlib
-Requires-Dist: pandas
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: plotly
-Requires-Dist: nbformat
-Requires-Dist: ipywidgets
+Requires-Dist: pandas<3,>=2
+Requires-Dist: numpy>=2
+Requires-Dist: matplotlib<4.0,>=3
+Requires-Dist: scipy<2,>=1
+Requires-Dist: plotly<6,>=5
+Requires-Dist: nbformat<6,>=5
+Requires-Dist: ipywidgets<9,>=8
+Requires-Dist: tqdm<5,>=4
+Requires-Dist: requests<3,>=2
 Requires-Dist: IPython
 Description-Content-Type: text/markdown
 

lunapi-1.2.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+lunapi-1.2.0.dist-info/RECORD,,
+lunapi-1.2.0.dist-info/WHEEL,sha256=CQCn-Gg7FyA1vyNSzvE34YdeHxf8WzJQKMn4oS65uIg,115
+lunapi-1.2.0.dist-info/METADATA,sha256=1-TAzaUSJf5OCha4HlTOS8dNcBMH5QAC9dmm3rxLyB0,1519
+lunapi-1.2.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+lunapi/lunapi0.cpython-310-darwin.so,sha256=hEG3vwwnr0X3rE2yhuedfm7IM0wDSuq4vOja8qIA9jc,19155712
+lunapi/__init__.py,sha256=cDep9d2N4KKUt81AzHUyFsuRdGwxCD1rqqFmptsAqsk,352
+lunapi/lunapi1.py,sha256=oSN4_0zEW5tKzTEfvp5Fc6qdsJPu0_qZdaG-d5hhZu8,92343
+lunapi/lunapi0.cpp,sha256=nQ5cwNdm4fvZ5TSDSxrgWu8Luw1r6NyDsvDWu9sLv7I,13053

{lunapi-0.1.1.dist-info → lunapi-1.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.9.4
+Generator: scikit-build-core 0.10.7
 Root-Is-Purelib: false
 Tag: cp310-cp310-macosx_10_9_x86_64
 

lunapi-0.1.1.dist-info/RECORD

@@ -1,8 +0,0 @@
-lunapi/lunapi0.cpython-310-darwin.so,sha256=1CbbnMT5fkk7UrU7vQ0ENzW6ZzF74IF85YwjyfT8lCo,18463864
-lunapi/__init__.py,sha256=cDep9d2N4KKUt81AzHUyFsuRdGwxCD1rqqFmptsAqsk,352
-lunapi/lunapi1.py,sha256=hzz8h9G2SEg2WIW-eN1oF6JKPZGZcGP4nSWvtf9iToM,90993
-lunapi/lunapi0.cpp,sha256=BCVMWAyJNKM8mnUFU7yRioH2TGyph5iIt85wxBE8kKo,12728
-lunapi-0.1.1.dist-info/RECORD,,
-lunapi-0.1.1.dist-info/WHEEL,sha256=krbo6XhnUQXR8ZQGAdjyrn-0wATirW0sbgQtk6A0vDg,114
-lunapi-0.1.1.dist-info/METADATA,sha256=qlb2AHZBxKUVFvm_ePq5TWBd_YRqZWmlTcAtl8V4zZE,1422
-lunapi-0.1.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149