h5 option for data input

fhd_core/setup_metadata/fhd_path_setup.pro

@@ -5,6 +5,7 @@ FUNCTION fhd_path_setup,file_path_vis,data_directory=data_directory,filename=fil
 IF Keyword_Set(file_path_vis) THEN BEGIN
     filename=file_basename(file_path_vis,'.sav',/fold_case) ;visibilities may be stored in an IDL save file, instead of uvfits
     filename=file_basename(filename,'.uvfits',/fold_case)
+    filename=file_basename(filename,'.h5',/fold_case)
     filename=file_basename(filename,'_cal',/fold_case) ;sometimes "_cal" is present, sometimes not.
     data_directory=file_dirname(file_path_vis)
 ENDIF

fhd_core/setup_metadata/fhd_struct_init_obs.pro

@@ -9,13 +9,11 @@ FUNCTION fhd_struct_init_obs,file_path_vis,hdr,params,layout,dimension=dimension
     grid_nfreq_avg=grid_nfreq_avg,_Extra=extra
 ;initializes the structure containing frequently needed parameters relating to the observation
 IF N_Elements(instrument) EQ 0 THEN instrument='mwa' ELSE instrument=StrLowCase(instrument)
-obsname=file_basename(file_basename(file_path_vis,'.uvfits',/fold_case),'_cal',/fold_case)
+obsname=file_basename(file_basename(file_path_vis,'.uvfits',/fold_case),'.h5',/fold_case)
 git,'describe',result=code_version,repo_path=rootdir('fhd'),args='--long --dirty'
 IF N_Elements(code_version) GT 0 THEN code_version=code_version[0] ELSE code_version=''
 
 IF N_Elements(n_pol) EQ 0 THEN n_pol=hdr.n_pol
-pol_names=['XX','YY','XY','YX','I','Q','U','V']
-
 IF Tag_exist(layout, "n_antenna") THEN BEGIN
     n_tile=layout.n_antenna 
 ENDIF ELSE BEGIN
@@ -162,7 +160,7 @@ params.antenna1 = tile_A
 params.antenna2 = tile_B
 
 meta=fhd_struct_init_meta(file_path_vis,hdr,params,layout,degpix=degpix,dimension=dimension,elements=elements,$
-    n_tile=n_tile,instrument=instrument,pol_names=pol_names,meta_data=meta_data,meta_hdr=meta_hdr,_Extra=extra)
+    n_tile=n_tile,instrument=instrument,meta_data=meta_data,meta_hdr=meta_hdr,_Extra=extra)
 
 IF N_Elements(meta_data) EQ 0 THEN meta_data=Ptr_new() ELSE meta_data=Ptr_new(meta_data)
 IF N_Elements(meta_hdr) EQ 0 THEN meta_hdr=Ptr_new() ELSE meta_hdr=Ptr_new(meta_hdr)
@@ -181,6 +179,7 @@ FOR ti=0,N_Elements(time_cut)<2-1 DO BEGIN
     IF ti_end GE ti_start THEN time_use[ti_start:ti_end]=0
 ENDFOR
 n_time_cut = n_time - Total(time_use)
+
 tile_use1=intarr(n_tile)
 FOR pol_i=0,n_pol-1 DO BEGIN
     tile_use_i=where(*(meta.tile_flag[pol_i]) EQ 0,n_use)
@@ -206,7 +205,7 @@ IF dimension GT 4096 THEN BEGIN
         double_precision=1
     ENDIF
 ENDIF
-
+pol_names=['XX','YY','XY','YX','I','Q','U','V']
 healpix={nside:Long(nside),ind_list:String(ind_list),n_pix:Long(n_hpx),n_zero:Long(n_zero_hpx)}
 
 arr={tile_A:Long(tile_A),tile_B:Long(tile_B),bin_offset:Long(bin_offset),Jdate:meta.Jdate,freq:Double(frequency_array),fbin_i:Long(freq_bin_i),$
@@ -216,7 +215,7 @@ struct={code_version:String(code_version),instrument:String(instrument),obsname:
     kpix:Float(kbinsize),degpix:Float(degpix),obsaz:meta.obsaz,obsalt:meta.obsalt,obsra:meta.obsra,obsdec:meta.obsdec,$
     zenra:meta.zenra,zendec:meta.zendec,obsx:meta.obsx,obsy:meta.obsy,zenx:meta.zenx,zeny:meta.zeny,$
     phasera:meta.phasera,phasedec:meta.phasedec,orig_phasera:meta.orig_phasera,orig_phasedec:meta.orig_phasedec,$
-    n_pol:Fix(n_pol,type=2),n_tile:Long(n_tile),n_tile_flag:Long(n_flag),n_freq:Long(n_freq),n_freq_flag:0L,n_time:Long(n_time),n_time_flag:Long(n_time_cut),$
+    n_pol:Fix(n_pol,type=2),n_tile:Long(n_tile),n_tile_flag:Long(n_flag),n_freq:Long(n_freq),n_freq_flag:0L,n_time:Long(n_time),n_time_flag:n_time_cut,$
     n_vis:Long(n_vis),n_vis_in:Long(n_vis_in),n_vis_raw:Long(n_vis_raw),nf_vis:Long(n_vis_arr),primary_beam_area:Ptrarr(4),primary_beam_sq_area:Ptrarr(4),pol_names:pol_names,$
     jd0:meta.jd0,max_baseline:Double(max_baseline),min_baseline:Double(min_baseline),delays:meta.delays,lon:meta.lon,lat:meta.lat,alt:meta.alt,$
     freq_center:Float(freq_center),freq_res:Float(freq_res),time_res:Float(meta.time_res),astr:meta.astr,alpha:Float(spectral_index),$

fhd_core/setup_metadata/uvh5_read_layout.pro

@@ -0,0 +1,48 @@
+FUNCTION uvh5_read_dataset, fid, path
+    did = H5D_OPEN(fid, path)
+    data = H5D_READ(did)
+    H5D_CLOSE, did
+    RETURN, data
+END
+
+FUNCTION uvh5_read_layout, file_path_vis, _EXTRA=extra
+
+    fid = H5F_OPEN(file_path_vis)
+
+    ant_names     = uvh5_read_dataset(fid, '/Header/antenna_names')
+    ant_numbers   = uvh5_read_dataset(fid, '/Header/antenna_numbers')
+    ant_positions = uvh5_read_dataset(fid, '/Header/antenna_positions')
+
+    latitude  = uvh5_read_dataset(fid, '/Header/latitude')
+    longitude = uvh5_read_dataset(fid, '/Header/longitude')
+    altitude  = uvh5_read_dataset(fid, '/Header/altitude')
+
+    telescope_name = uvh5_read_dataset(fid, '/Header/telescope_name')
+
+    H5F_CLOSE, fid
+
+    nant = N_ELEMENTS(ant_numbers)
+
+    ; IDL/HDF5 dimension order can be reversed, so make sure positions are [3, nant].
+    pos_dims = SIZE(ant_positions, /DIMENSIONS)
+    IF pos_dims[0] NE 3 THEN ant_positions = TRANSPOSE(ant_positions)
+
+    ; Build a layout structure with the fields FHD usually needs.
+    ; UVH5 antenna_positions are ECEF positions relative to the telescope location,
+    ; not an AIPS AN binary table. pyuvdata documents that telescope.antenna_positions
+    ; are ECEF positions relative to telescope.location. :contentReference[oaicite:2]{index=2}
+
+    layout = { $
+        n_antenna: nant, $
+        antenna_names: ant_names, $
+        antenna_numbers: ant_numbers, $
+        antenna_positions: ant_positions, $
+        latitude: latitude, $
+        longitude: longitude, $
+        altitude: altitude, $
+        telescope_name: telescope_name $
+    }
+
+    RETURN, layout
+
+END

fhd_core/visibility_manipulation/uvfits_read.pro

@@ -1,7 +1,7 @@
 PRO uvfits_read,hdr,params,layout,vis_arr,vis_weights,file_path_vis=file_path_vis,n_pol=n_pol,silent=silent,$
     restore_vis_savefile=restore_vis_savefile,reorder_visibilities=reorder_visibilities,$
     vis_time_average=vis_time_average,vis_freq_average=vis_freq_average,error=error,$
-    uvfits_spectral_dimension=uvfits_spectral_dimension,_Extra=extra
+    uvfits_spectral_dimension=uvfits_spectral_dimension,freq_split=freq_split,_Extra=extra
 ;set n_pol=0 to not return any data, only header and parameters
 
 IF Strpos(file_path_vis,'.sav') EQ -1 THEN file_path_vis_sav=file_path_vis+".sav" ELSE file_path_vis_sav=file_path_vis
@@ -24,16 +24,28 @@ ENDIF ELSE BEGIN
     ENDIF
 
     t_readfits=Systime(1)
-    lun = fxposit(file_path_vis, 0,/readonly)
-    data_struct=mrdfits(lun,0,data_header0,/silent)
+    ext = STRLOWCASE(FILE_BASENAME(file_path_vis))
+    if STRMATCH(ext, '*.uvh5') OR STRMATCH(ext, '*.h5') THEN BEGIN
+        if N_elements(freq_split) EQ 0 THEN BEGIN
+            data_struct = uvh5_mrdfits(file_path_vis, data_header0)
+        endif else begin
+            chan0=freq_split*2
+            data_struct = uvh5_mrdfits(file_path_vis, data_header0, chan0=chan0, num_chans=2, freq_ref=freq_ref)
+            freq_split = freq_ref
+        endelse
+    ENDIF ELSE BEGIN
+        lun = fxposit(file_path_vis, 0,/readonly)
+        data_struct=mrdfits(lun,0,data_header0,/silent)
+    ENDELSE
+
     hdr=vis_header_extract(data_header0, params = data_struct.params,error=error,_Extra=extra)    
     IF Keyword_Set(error) THEN RETURN
     IF N_Elements(n_pol) EQ 0 THEN n_pol=hdr.n_pol ELSE n_pol=n_pol<hdr.n_pol
 
     params=vis_param_extract(data_struct.params,hdr,_Extra=extra)
     t_readfits=Systime(1)-t_readfits
     print,"Time reading UVFITS files and extracting header: "+Strn(t_readfits)
-    
+
     data_array=Temporary(data_struct.array) 
     data_struct=0. ;free memory
 
@@ -87,12 +99,16 @@ ENDIF ELSE BEGIN
 
     ;; now read extensions one by one until we find the antenna table
     t_read_ant=Systime(1)
-    ext_name = ''
-    while ext_name ne 'AIPS AN' do begin
-        ext_data = mrdfits(lun, 0, ext_header)
-        ext_name=strtrim(sxpar(ext_header, 'extname'))
-    endwhile
-    layout = fhd_struct_init_layout(ext_header, ext_data,_Extra=extra)
+    IF STRMATCH(ext, '*.uvh5') OR STRMATCH(ext, '*.h5') THEN BEGIN
+        layout = uvh5_read_layout(file_path_vis, _Extra=extra)
+    ENDIF ELSE BEGIN
+        ext_name = ''
+        while ext_name ne 'AIPS AN' do begin
+            ext_data = mrdfits(lun, 0, ext_header)
+            ext_name=strtrim(sxpar(ext_header, 'extname'))
+        endwhile
+        layout = fhd_struct_init_layout(ext_header, ext_data,_Extra=extra)
+    ENDELSE
     t_read_ant=Systime(1)-t_read_ant
     print,"Time finding and reading antenna table in UVFITS file and extracting header: "+Strn(t_read_ant) 
 
@@ -108,8 +124,6 @@ ENDIF ELSE BEGIN
         vis_average,vis_arr,vis_weights,params,hdr,vis_time_average=vis_time_average,vis_freq_average=vis_freq_average,timing=t_averaging
         IF ~Keyword_Set(silent) THEN print,"Visibility averaging time: "+Strtrim(String(t_averaging),2)
     ENDIF
-
-
-
+
 ENDELSE    
 END