Introduce sugar for callbacks

5 files changed, 50 insertions, 44 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
index 4702c670..c71b9f22 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
@@ -37,11 +37,17 @@ def callbacks():
         progress = progress,
         mprint = mprint
     )
-    
+
+def uses(*funcs):
+    """
+    Some sugar
+    """
+    return [callbacks()[func] for func in funcs]
+
 # ----- Minor test cases:
 
 if __name__ == '__main__':
-    logging.basicConfig(level=logging.DEBUG)
+    # logging.basicConfig(level=logging.DEBUG)
     logging.debug("Test %i" % (1))
     d = callbacks()['debug']
     d("TEST")
@@ -49,3 +55,19 @@ if __name__ == '__main__':
     wrln("Hello %i" % 34)
     progress = callbacks()['progress']
     progress("I am half way",50,100)
+    list = [0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15,
+            0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15,
+            0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15,
+            0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15,
+            0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15]
+    mprint("list",list)
+    matrix = [[1,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15],
+            [2,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15],
+            [3,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15],
+            [4,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15],
+            [5,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15],
+            [6,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15]]
+    mprint("matrix",matrix)
+    ix,dx = uses("info","debug")
+    ix("ix")
+    dx("dx")
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index d3792570..62f7be47 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -74,46 +74,39 @@ def f_init(q):
 
 # Calculate the kinship matrix from G (SNPs as rows!), returns K
 #
-def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True):
-   numThreads = None
-   if numThreads:
-      numThreads = int(numThreads)
+def kinship(G,uses,computeSize=1000,numThreads=None,useBLAS=False):
+   progress,debug,info,mprint = uses('progress','debug','info','mprint')
+
    matrix_initialize(useBLAS)
-   
-   sys.stderr.write(str(G.shape)+"\n")
+
+   mprint("G",G)
    n = G.shape[1] # inds
    inds = n
    m = G.shape[0] # snps
    snps = m
-   sys.stderr.write(str(m)+" SNPs\n")
+   info("%i SNPs" % (m))
    assert snps>inds, "snps should be larger than inds (%i snps, %i inds)" % (snps,inds)
 
    q = mp.Queue()
    p = mp.Pool(numThreads, f_init, [q])
    cpu_num = mp.cpu_count()
-   print "CPU cores:",cpu_num
-   print snps,computeSize
+   info("CPU cores: %i" % cpu_num)
    iterations = snps/computeSize+1
-   # if testing:
-   #    iterations = 8
-   # jobs = range(0,8) # range(0,iterations)
 
    results = []
-
    K = np.zeros((n,n))  # The Kinship matrix has dimension individuals x individuals
 
    completed = 0
    for job in range(iterations):
-      if verbose:
-         sys.stderr.write("Processing job %d first %d SNPs\n" % (job, ((job+1)*computeSize)))
+      info("Processing job %d first %d SNPs" % (job, ((job+1)*computeSize)))
       W = compute_W(job,G,n,snps,computeSize)
       if numThreads == 1:
          # Single-core
          compute_matrixMult(job,W,q)
          j,x = q.get()
-         if verbose: sys.stderr.write("Job "+str(j)+" finished\n")
+         debug("Job "+str(j)+" finished")
+         progress("kinship",j,iterations)
          K_j = x
-         # print j,K_j[:,0]
          K = K + K_j
       else:
          # Multi-core
@@ -123,39 +116,27 @@ def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True):
             time.sleep(0.1)
             try: 
                j,x = q.get_nowait()
-               if verbose: sys.stderr.write("Job "+str(j)+" finished\n")
+               debug("Job "+str(j)+" finished")
                K_j = x
-               # print j,K_j[:,0]
                K = K + K_j
                completed += 1
+               progress("kinship",completed,iterations)
             except Queue.Empty:
                pass
          
    if numThreads == None or numThreads > 1:
-      # results contains the growing result set
       for job in range(len(results)-completed):
          j,x = q.get(True,15)
-         if verbose: sys.stderr.write("Job "+str(j)+" finished\n")
+         debug("Job "+str(j)+" finished")
          K_j = x
-         # print j,K_j[:,0]
          K = K + K_j
          completed += 1
+         progress("kinship",completed,iterations)
 
    K = K / float(snps)
-   
-   # outFile = 'runtest.kin'
-   # if verbose: sys.stderr.write("Saving Kinship file to %s\n" % outFile)
-   # np.savetxt(outFile,K)
-
-   # if saveKvaKve:
-   #    if verbose: sys.stderr.write("Obtaining Eigendecomposition\n")
-   #    Kva,Kve = linalg.eigh(K)
-   #    if verbose: sys.stderr.write("Saving eigendecomposition to %s.[kva | kve]\n" % outFile)
-   #    np.savetxt(outFile+".kva",Kva)
-   #    np.savetxt(outFile+".kve",Kve)
    return K      
 
-def kvakve(K, uses):
+def kvakve(K,uses):
    """
    Obtain eigendecomposition for K and return Kva,Kve where Kva is cleaned
    of small values < 1e-6 (notably smaller than zero)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 2076bc84..5182e73c 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -395,7 +395,7 @@ def calculate_kinship_new(genotype_matrix, temp_data=None):
     print("call genotype.normalize")
     G = np.apply_along_axis( genotype.normalize, axis=0, arr=genotype_matrix)
     print("call calculate_kinship_new")
-    return kinship(G.T),G # G gets transposed, we'll turn this into an iterator (FIXME)
+    return kinship(G.T,uses),G # G gets transposed, we'll turn this into an iterator (FIXME)
 
 def calculate_kinship_old(genotype_matrix, temp_data=None):
     """
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 324c4f2c..e3e8659c 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -25,6 +25,7 @@ from lmm import gn2_load_redis, calculate_kinship_old
 from kinship import kinship, kinship_full
 import genotype
 import phenotype
+from standalone import uses
 
 usage = """
 python runlmm.py [options] command
@@ -193,7 +194,7 @@ elif cmd == 'kinship':
         k2 = round(K2[0][0],4)
     
     print "Genotype",G.shape, "\n", G
-    K3 = kinship(G.T)
+    K3 = kinship(G.T,uses)
     print "third Kinship method",K3.shape,"\n",K3
     sys.stderr.write(options.geno+"\n")
     k3 = round(K3[0][0],4)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
index 705da21f..538007f1 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
@@ -12,11 +12,13 @@ import numpy as np
 import sys
 import logging
 
+# logger = logging.getLogger(__name__)
+logger = logging.getLogger('lmm2')
 logging.basicConfig(level=logging.DEBUG)
 np.set_printoptions(precision=3,suppress=True)
 
 def progress(location, count, total):
-    logging.info("Progress: %s %d%%" % (location,round(count*100.0/total)))
+    logger.info("Progress: %s %d%%" % (location,round(count*100.0/total)))
 
 def mprint(msg,data):
     """
@@ -36,11 +38,11 @@ def callbacks():
     return dict(
         write = sys.stdout.write,
         writeln = print,
-        debug = logging.debug,
-        info = logging.info,
-        warning = logging.warning,
-        error = logging.error,
-        critical = logging.critical,
+        debug = logger.debug,
+        info = logger.info,
+        warning = logger.warning,
+        error = logger.error,
+        critical = logger.critical,
         progress = progress,
         mprint = mprint
     )